diff --git a/RELEASE_NOTES b/RELEASE_NOTES index f4454f0b91e4..26d8721fa486 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,102 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 16,628 easyconfig files, for 2,995 different software packages, +The latest version of easybuild-easyconfig provides 17,098 easyconfig files, for 3,085 different software packages, incl. 39 different (compiler) toolchains. +v4.7.2 (27 May 2023) +-------------------- + +update/bugfix release + +- added easyconfigs for intel/2023.03 (#17676) +- added example easyconfig files for 89 new software packages: + - AGeNT (#17864), anndata (#17677), Annocript (#17910), avro-cpp (#17527), batchgenerators (#17833), + BoltzTraP2 (#17742), Braindecode (#17913), build (#17776), casacore (#15499), Casanovo (#17735, #17736), + CASPR (#17606), CellChat (#17856), CellOracle (#17507), CLIP (#17782), CodingQuarry (#17682), ColabFold (#17751), + CopyKAT (#17646), CPC2 (#17849), cppzmq (#17601), dask-labextension (#17882), DIALOGUE (#17696), DiCE-ML (#17591), + ESPResSo (#17709), Evcxr-REPL (#17831), EZC3D (#17832), funannotate (#17588), FunGAP (#17652), GATB-Core (#17635), + GenMap (#17746), GimmeMotifs (#17507), GLI (#17793), GOBNILP (#17639), h5netcdf (#17835), HD-BET (#17833), + HTSplotter (#17369, #17586), ipympl (#17613), IsoSeq (#17791), KrakenUniq (#17569), LIANA (#17928), + libWallModelledLES (#17480), LoRDEC (#17635), M3GNet (#17555), mandrake (#17394), mctc-lib (#16760), MOABB (#17913), + MRPRESSO (#17925), ont-guppy (#17477, #17828), OptaDOS (#17777), PALEOMIX (#17912), PGPLOT (#15496), + PICI-LIGGGHTS (#17710), pod5-file-format (#17776), powerlaw (#17647), pp-sketchlib (#17397), + py3Dmol (#17752), pytesseract (#17898), pytest-cpp (#17966), pytest-flakefinder (#17966), Python-bundle (#17626), + python-xxhash (#17844), PyTorch-bundle (#17540), qnorm (#17507), R-MXM (#17667), R-transport (#17642, #17968), + Raven (#15833), ReaxFF (#17780), ripunzip (#17959), RPostgreSQL (#17739), rustworkx (#17857), Scalene (#16472), + sceasy (#17677), SCIP (#17639), Simple-DFTD3 (#16760), SMAP (#17672), SoPlex (#17639), SoupX (#17851), + spektral (#15551), synthcity (#17623), sysbench (#17643), tantan (#17681), thirdorder (#17703), TOPAS (#17553), + Triplexator (#17866), tRNAscan-SE (#17680, #17800), turbinesFoam (#17917), unicore-uftp (#17665), vispr (#17606), + WCSLIB (#15497), ZIMPL (#17639) +- added additional easyconfigs for various supported software packages, including: + - Abseil v20230125.2, AlphaFold v2.3.1 + v2.3.4, Arrow v11.0.0, arrow-R v11.0.0.3, astropy v5.2.2, awscli v2.11.21, + Bismark v0.24.0, biom-format v2.1.14, Blender v3.5.0, Blosc2 v2.8.0, Bottleneck v1.3.7, breseq v0.38.1, + bwa-meth v0.2.6, buildenv default for foss/2022b + CUDA 12.0.0, Cantera v2.6.0, CapnProto v0.10.3, CASTEP v22.11, + Clang v15.0.5, CLHEP v2.4.6.4, CMake v3.26.3, CMSeq v1.0.4, coverage v7.2.3, CP2K v9.1 + v2022.1, CPLEX v22.1.1, + CREST v2.11.2, cURL v8.0.1, CuPy v11.4.0, DBus v1.15.4, DBG2OLC v20200724, dlb v3.3.1, double-conversion v3.3.0, + Doxygen v1.9.7, expat v2.5.0, FASTA v36.3.8i, FHI-aims v221103, fio v3.34, Fiona v1.9.2, Flask v2.2.3, fmt v10.0.0, + freeglut v3.4.0, FUSE v3.14.1, GapFiller v2.1.2, GCC 12.3.0 + 13.1.0, GDCM v3.0.21, GitPython v3.1.31, Go v1.20.4, + googletest v1.13.0, gpustat v1.1, Guile v3.0.9, Gurobi v10.0.1, Harminv v1.4.2, Highway v1.0.4, IgBlast v1.21.0, + Imath v3.1.7, infercnvpy v0.4.2, IQ-TREE v2.2.2.3, jax v0.3.25, jupyterlmod v4.0.3, Kalign v3.3.5, + L_RNA_scaffolder v20190530, libaio v0.3.113, libarchive v3.6.2, libctl v4.5.1, libdeflate v1.8, libgcrypt v1.10.1, + libGridXC v1.1.0, libjpeg-turbo v2.1.5.1, libmaus2 v2.0.499, libopus v1.4, libpng v1.6.39, libPSML v1.1.12, + libRmath v4.2.1, libsigc++ v3.4.0, LibTIFF v4.5.0, libunistring v1.1, libxc v6.1.0, libxml2 v2.11.4, + libxslt v1.1.38, lifelines v0.27.4, lxml v4.9.2, make v4.4.1, MariaDB v10.11.2, Meep v1.26.0, MetaPhlAn v4.0.6, + mold v1.11.0, MPB v1.11.1, muParser v2.3.4, NAG v7.1, NAGfor v7.1, nano v7.2, NASM v2.16.01, ncurses v6.4, + netcdf4-python v1.6.3, networkx v2.8.8, NSS v3.89.1, numexpr v2.8.4, nvtop v3.0.1, OpenEXR v3.1.7, OpenMM v8.0.0, + Pandoc v3.1.2, ParaView v5.11.0, PCRE2 v10.42, PhyloPhlAn v3.0.3, phyx v1.3, picard v3.0.0, Pint v0.20.1, + pkgconf v1.9.5, PostgreSQL v15.2, PROJ v9.2.0, Proteinortho v6.2.3, protobuf v23.0, protobuf-python v4.23.0, + pydantic v1.10.4, pyFFTW v0.13.1, PyGEOS v0.14, Pyomo v6.5.0, pyparsing v3.0.9, pyperf v2.6.0, pyproj v3.5.0, + pytest v7.2.2, PYTHIA v8.309, Qtconsole v5.4.0, R-bundle-Bioconductor v3.16, R-tesseract v5.1.0, RE2 v2023-03-01, + ReFrame v4.2.0, RepeatMasker v4.1.5, RevBayes v1.2.1, rgdal v1.6-6, rioxarray v0.14.0, rocm-smi v5.4.4, + ROOT v6.26.10, Rtree v1.0.1, scib v1.1.3, scikit-build v0.17.2, Seaborn v0.12.2, SHAP v0.41.0, Shapely v2.0.1, + ShengBTE v1.5.0, SLiM v4.0.1, snappy v1.1.10, spdlog v1.11.0, spglib v2.0.2, spglib-python v2.0.2, SQLite v3.42.0, + Subread v2.0.4, Tcl v8.6.13, tcsh v6.24.05, torchtext v0.14.1, trimesh v3.21.5, UCC-CUDA v1.1.0, utf8proc v2.8.0, + Vim v9.0.1434, vsc-mympirun v5.3.1, WRF v4.4.1, xmlf90 v1.5.6, xxHash v0.8.1, XZ v5.4.2, zsh v5.9, zstd v1.5.5 +- minor enhancements, including: + - add local::lib extension to Perl 5.34.0 (#17679) + - install shared libraries for tesseract (#17721) + - add additional extensions to recent R easyconfigs: word2vec, tau, quanteda, ... (#17738) + - add extensions to R-bundle-Bioconductor 3.15: deepSNV (#17852) + - add extensions to R 4.2.x: dlm (#17640), PMA + unikn + ppcor (#17695), tvem (#17729), epitools (#17852) +- various bug fixes, including: + - add patch for UCC 1.1.0 for multiple component paths (#17255) + - fix configure step for ELSI 2.5.0+ (#17288) + - switch bamtofastq to Cargo easyblock (#17595) + - add missing OpenJPEG dependency for recent GDAL versions (#17599) + - fix CodAn bin/* executable permissions for all users #(#17607) + - upgrade traitlets, ipywidgets, and widgetsnbextension + downgrade jupyterlab_widgets extensions in IPython v8.5.0 to fix known issues (#17612) + - add patch for GPAW-22.8.0 with 2022a toolchain to make test tolerance a bit less strict (#17618) + - add alternative checksum for MONAI 1.0.1 (#17628) + - fix paths to Perl modules in MAKER v3.01.04 (#17629) + - add missing dependencies and add patch for fix incorrect ids for BRAKER v2.1.6 (#17631) + - explicitely disable mpi/python in Boost (intel-compilers/2021.4.0) (#17638) + - remove LLVM build dependency from TensorFlow easyconfigs (#17641) + - update easyconfig for Longshot 0.4.5 to use Cargo easyblock (#17666) + - fix homepage in ELPA easyconfigs (due to switch to new domain) (#17697) + - add patch for scipy 1.10.1 extension in SciPy-bundle 2023.02 to fix broken test (#17713) + - use CUDA variant of OpenMM 7.5.1 as dependency for AlphaFold 2.3.0 (#17717) + - exclude flaky test_optim for PyTorch 1.12.1 + make excluded tests for PyTorch 1.12.1 consistent (#17726, #17730, #17731, #17737) + - add missing PCRE dependency for InterProScan 5.55-88.0 (#17762) + - fix building Python bindings of DGL, requires static libs (#17764) + - only use QEF gitlab source url for QuantumESPRESSO itself (#17766) + - add egg file to OpenCV 4.6.0 python package for pip + pkgconfig file (#17779) + - fix broken source URL for AOCC 4.0.0 (#17794) + - specify source_urls inside exts_default_options in Seurat easyconfigs to ensure correct name expansion for the archived packages (#17830) + - add Doxygen build dependency to X11 (#17842) + - FLINT needs BLAS so move it up from GCC level (#17868) + - fix broken tarball links for ispc 1.6, 1.10, and 1.12 easyconfigs (#17875) + - add dependency on PycURL to JupyterHub-3.0.0-GCCcore-11.3.0.eb (#17887) + - add historical repo paths to install cmd for old versions of texlive (#17893) + - add missing FastTreeMP binary for FastTree (#17897) + - add checksum for arm64 source tarball for Go 1.18.3 (#17903) + - add patch to fix test_quantization in PyTorch 1.12.1 (#17908) + - add make 4.3 as build dependency for recent OpenBLAS versions (#17924) +- other changes: + - bump versions in Java wrappers to latest builds that include ppc64le: Java/8.362, Java/11.0.8, Java/17.0.6 (#17775) + - move Arb and polymake to gfbf/foss since FLINT is now at gfbf/foss (#17869) + v4.7.1 (March 20th 2023) ------------------------ diff --git a/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb b/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb new file mode 100644 index 000000000000..c176dbde77c5 --- /dev/null +++ b/easybuild/easyconfigs/a/AGeNT/AGeNT-3.0.6.eb @@ -0,0 +1,69 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +# JAR files are in a subdirectory with other stuff, so use Binary +easyblock = 'Binary' + +name = 'AGeNT' +version = '3.0.6' + +homepage = 'https://www.agilent.com/en/product/next-generation-sequencing/' +homepage += 'hybridization-based-next-generation-sequencing-ngs/ngs-software/agent-232879' +description = """The Agilent Genomics NextGen Toolkit (AGeNT) is a Java-based software +module that processes the read sequences from targeted high-throughput sequencing data +generated by sequencing Agilent SureSelect and HaloPlex libraries. + +The Trimmer utility of the AGeNT module processes the read sequences to identify and +remove the adaptor sequences and extracts dual molecular barcodes (for SureSelect XT HS2). + +The LocatIt utility of the AGeNT module processes the Molecular Barcode (MBC) information +from HaloPlex HS, SureSelect XT HS, and SureSelect XT HS2 Illumina sequencing runs with +options to either mark or merge duplicate reads and output in BAM file format. The Illumina +InterOp libraries are a set of common routines used for reading InterOp metric files +produced by Illumina sequencers including NextSeq 1k/2k. These libraries are backwards +compatible and capable of supporting prior releases of the software, with one exception: +GA systems have been excluded.""" + +software_license = 'LicenseVeryRestrictive' +# For Research Use Only. Not for use in diagnostic procedures. + +toolchain = SYSTEM + +builddependencies = [ + ('UnZip', '6.0', '', ('GCCcore', '10.3.0')), +] +dependencies = [ + ('Java', '11'), +] + +# Fill the form at https://explore.agilent.com/AGeNT-Software-Download-Form +# to get the zip file. +sources = ['AGeNT_%(version)s.zip'] +checksums = ['746e4445567ee41b7ced5cab3cd252d27d8f6f9eab56766e5d7ca74894e3db73'] + +extract_sources = False + +install_cmd = 'unzip ' + sources[0] + ' && ' +install_cmd += 'cp -ar *.html *.md agent/* %(installdir)s/ && ' +install_cmd += 'chmod -x %(installdir)s/*.txt && ' +install_cmd += 'chmod -x %(installdir)s/*.md && ' +install_cmd += 'rm -f %(installdir)s/*.cmd && ' +install_cmd += 'rm -f %(installdir)s/*.html && ' +install_cmd += 'mkdir %(installdir)s/bin && ' +install_cmd += 'mv %(installdir)s/*.sh %(installdir)s/bin/ && ' +install_cmd += 'ln -s ../lib %(installdir)s/bin/lib && ' +install_cmd += 'sed -i "s@ lib/@ ../lib/@" %(installdir)s/bin/*.sh' + +sanity_check_paths = { + 'files': ['bin/agent.sh'], + 'dirs': ['bin', 'lib'] +} + +sanity_check_commands = ["agent.sh"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb index aca9ebc5b59d..b2b557cf8919 100644 --- a/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb @@ -8,7 +8,7 @@ description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0 # already specified as the toolchain. toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -source_urls = ['http://developer.amd.com/wordpress/media/files/'] +source_urls = ['https://download.amd.com/developer/eula/aocc-compiler/'] sources = ['aocc-compiler-%(version)s.tar'] checksums = ['2729ec524cbc927618e479994330eeb72df5947e90cfcc49434009eee29bf7d4'] diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2022b.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2022b.eb new file mode 100644 index 000000000000..d2486e7b79ee --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gfbf-2022b.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Flask', '2.2.3'), + ('matplotlib', '3.7.0'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.0.2'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.8.2', { + 'checksums': ['77f03f4554392558700295e05aed0b1096a20d4a60a4f3ddcde58b0c31c8fca2'], + }), + ('ase', version, { + 'patches': [ + 'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch', + 'ASE-3.22.1-Compatibility-with-pytest-part-2.patch', + 'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch', + 'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch', + ], + 'checksums': [ + '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432', # ase-3.22.1.tar.gz + # ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch + '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac', + # ASE-3.22.1-Compatibility-with-pytest-part-2.patch + '3a3473912f5f96ffc625119d87227781ba4ea581de15d4af6a58ba960cdf4601', + # ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch + 'c1cb07160b063d432f098efd40dd4b3c9f015b7966572c838a908613a482e0c8', + # ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch + '2a05f98291dc970cb759904988783d1ecc3512ba6a0da852af1d3205667b398d', + ], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gomkl-2021a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gomkl-2021a.eb new file mode 100644 index 000000000000..cefd29a89577 --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-gomkl-2021a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Flask', '1.1.4'), + ('matplotlib', '3.4.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '1.16.1'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.6.1', { + 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], + }), + ('ase', version, { + 'checksums': ['004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..ac3526452edc --- /dev/null +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'Abseil' +version = '20230125.2' + +homepage = 'https://abseil.io/' +description = """Abseil is an open-source collection of C++ library code designed to augment the +C++ standard library. The Abseil library code is collected from Google's own +C++ code base, has been extensively tested and used in production, and is the +same code we depend on in our daily coding lives.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++17'} + +source_urls = ['https://github.com/abseil/abseil-cpp/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['9a2b5752d7bfade0bdeee2701de17c9480620f8b237e1964c1b9967c75374906'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['lib/libabsl_base.%s' % SHLIB_EXT], + 'dirs': ['include/absl'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..b76e53de45bd --- /dev/null +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'Abseil' +version = '20230125.3' + +homepage = 'https://abseil.io/' +description = """Abseil is an open-source collection of C++ library code designed to augment the +C++ standard library. The Abseil library code is collected from Google's own +C++ code base, has been extensively tested and used in production, and is the +same code we depend on in our daily coding lives.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++17'} + +source_urls = ['https://github.com/abseil/abseil-cpp/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['5366d7e7fa7ba0d915014d387b66d0d002c03236448e1ba9ef98122c13b35c36'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['lib/libabsl_base.%s' % SHLIB_EXT], + 'dirs': ['include/absl'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb index 348e3a6aaed1..b37b644450f2 100644 --- a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.0-foss-2021b-CUDA-11.4.1.eb @@ -29,7 +29,7 @@ dependencies = [ ('UCX-CUDA', '1.11.2', versionsuffix), ('cuDNN', '8.2.2.26', versionsuffix, SYSTEM), ('NCCL', '2.10.3', versionsuffix), - ('OpenMM', '7.5.1', '-DeepMind-patch'), + ('OpenMM', '7.5.1', '%(versionsuffix)s-DeepMind-patch'), ] # commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..6dc2fe0aa601 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,169 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.3.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + # required for installing dm-tree + ('Bazel', '5.1.1'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('TensorFlow', '2.11.0', versionsuffix), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.5'), + ('jax', '0.3.25', versionsuffix), # also provides absl-py + ('UCX-CUDA', '1.12.1', versionsuffix), + ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM), + ('NCCL', '2.12.12', versionsuffix), + ('OpenMM', '8.0.0', versionsuffix), +] + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.3.0_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.1.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.3.1_use_openmm_7.7.0.patch', + ], + 'checksums': [ + '1161b2609fa896b16399b900ec2b813e5a0b363fe4e2b26bd826953ba234736a', # v2.3.1.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '5cff3fc7104e020ef546d23cb4fb1b8d6517562783f055cc55fc65fe2b0248d0', # AlphaFold-2.3.0_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + # AlphaFold-2.3.1_use_openmm_7.7.0.patch + 'd800bb085deac7edbe2d72916c1194043964aaf51b88a3b5a5016ab68a1090ec', + + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.8.1', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('chex', '0.1.6', { + 'checksums': ['adb5d2352b5f0d248ccf594be1b1bf9ee7a2bee2a57f0eac78547538d479b0e7'], + }), + ('tabulate', '0.9.0', { + 'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('dm-tree', '0.1.8', { + 'modulename': 'tree', + 'checksums': ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'], + }), + ('websocket-client', '1.5.1', { + 'modulename': 'websocket', + 'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'], + }), + ('docker', '6.0.1', { + 'checksums': ['896c4282e5c7af5c45e8b683b0b0c33932974fe6e50fc6906a0a83616ab3da97'], + }), + ('immutabledict', '2.2.3', { + 'checksums': ['0e1e8a3f2b3ff062daa19795f947e9ec7a58add269d44e34d3ab4319e1343853'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold*.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m openmm.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; +# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py +modextravars = { + 'TF_FORCE_UNIFIED_MEMORY': '1', + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '3', + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt + 'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb new file mode 100644 index 000000000000..565504238bb6 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1-foss-2022a.eb @@ -0,0 +1,159 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.3.1' + +homepage = 'https://deepmind.com/research/case-studies/alphafold' +description = "AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + # required for installing dm-tree + ('Bazel', '5.1.1'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('TensorFlow', '2.11.0'), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.5'), + ('jax', '0.3.25'), # also provides absl-py + ('OpenMM', '8.0.0'), +] + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/deepmind/alphafold/archive/refs/tags/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-2.0.0_fix-packages.patch', + 'AlphaFold-2.3.0_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-2.1.0_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.3.1_use_openmm_7.7.0.patch', + ], + 'checksums': [ + '1161b2609fa896b16399b900ec2b813e5a0b363fe4e2b26bd826953ba234736a', # v2.3.1.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + '826d2d1a5d6ac52c51a60ba210e1947d5631a1e2d76f8815305b5d23f74458db', # AlphaFold-2.0.0_fix-packages.patch + '5cff3fc7104e020ef546d23cb4fb1b8d6517562783f055cc55fc65fe2b0248d0', # AlphaFold-2.3.0_data-dep-paths.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', # AlphaFold-2.0.0_n-cpu.patch + '5363d403baf5ab73f4d3ddd72e19af9ff832de4b1d7ba25a5fbcc5846c1c890f', # AlphaFold-2.1.0_fix-scp-path.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', # AlphaFold-2.0.1_setup_rm_tfcpu.patch + # AlphaFold-2.3.1_use_openmm_7.7.0.patch + 'd800bb085deac7edbe2d72916c1194043964aaf51b88a3b5a5016ab68a1090ec', + + ], + 'start_dir': 'alphafold-%(version)s', + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.8.1', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('chex', '0.1.6', { + 'checksums': ['adb5d2352b5f0d248ccf594be1b1bf9ee7a2bee2a57f0eac78547538d479b0e7'], + }), + ('tabulate', '0.9.0', { + 'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('dm-tree', '0.1.8', { + 'modulename': 'tree', + 'checksums': ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'], + }), + ('websocket-client', '1.5.1', { + 'modulename': 'websocket', + 'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'], + }), + ('docker', '6.0.1', { + 'checksums': ['896c4282e5c7af5c45e8b683b0b0c33932974fe6e50fc6906a0a83616ab3da97'], + }), + ('immutabledict', '2.2.3', { + 'checksums': ['0e1e8a3f2b3ff062daa19795f947e9ec7a58add269d44e34d3ab4319e1343853'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), +] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %(builddir)s/alphafold-%(version)s/run_alphafold.py >> %(installdir)s/bin/run_alphafold.py", + "chmod a+x %(installdir)s/bin/run_alphafold*.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %(builddir)s/alphafold-%(version)s/scripts %(installdir)s/", + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH " + "python %(builddir)s/alphafold-%(version)s/run_alphafold_test.py", +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m openmm.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextravars = { + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_use_openmm_7.7.0.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_use_openmm_7.7.0.patch new file mode 100644 index 000000000000..ff3aa457201a --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.1_use_openmm_7.7.0.patch @@ -0,0 +1,240 @@ +# Add compatibility with OpenMM-7.7.0 +# The patch is based on the recipe from https://github.com/deepmind/alphafold/issues/404 +# Author: maxim-masterov (SURF) + +diff -Nru alphafold-2.3.1.orig/alphafold/relax/amber_minimize.py alphafold-2.3.1/alphafold/relax/amber_minimize.py +--- alphafold-2.3.1.orig/alphafold/relax/amber_minimize.py 2023-03-28 10:58:07.126241000 +0200 ++++ alphafold-2.3.1/alphafold/relax/amber_minimize.py 2023-03-28 11:24:17.380332000 +0200 +@@ -27,10 +27,10 @@ + import ml_collections + import numpy as np + import jax +-from simtk import openmm +-from simtk import unit +-from simtk.openmm import app as openmm_app +-from simtk.openmm.app.internal.pdbstructure import PdbStructure ++from openmm import * ++from openmm import unit ++from openmm import app as openmm_app ++from openmm.app.internal.pdbstructure import PdbStructure + + + ENERGY = unit.kilocalories_per_mole +@@ -47,7 +47,7 @@ + + + def _add_restraints( +- system: openmm.System, ++ system: System, + reference_pdb: openmm_app.PDBFile, + stiffness: unit.Unit, + rset: str, +diff -Nru alphafold-2.3.1.orig/alphafold/relax/cleanup.py alphafold-2.3.1/alphafold/relax/cleanup.py +--- alphafold-2.3.1.orig/alphafold/relax/cleanup.py 2023-03-28 10:58:07.126999000 +0200 ++++ alphafold-2.3.1/alphafold/relax/cleanup.py 2023-03-28 11:03:20.689464000 +0200 +@@ -20,8 +20,8 @@ + import io + + import pdbfixer +-from simtk.openmm import app +-from simtk.openmm.app import element ++from openmm import app ++from openmm.app import element + + + def fix_pdb(pdbfile, alterations_info): +diff -Nru alphafold-2.3.1.orig/alphafold/relax/cleanup_test.py alphafold-2.3.1/alphafold/relax/cleanup_test.py +--- alphafold-2.3.1.orig/alphafold/relax/cleanup_test.py 2023-03-28 10:58:07.127710000 +0200 ++++ alphafold-2.3.1/alphafold/relax/cleanup_test.py 2023-03-28 11:03:14.772207000 +0200 +@@ -17,7 +17,7 @@ + + from absl.testing import absltest + from alphafold.relax import cleanup +-from simtk.openmm.app.internal import pdbstructure ++from openmm.app.internal import pdbstructure + + + def _pdb_to_structure(pdb_str): +diff -Nru alphafold-2.3.1.orig/docker/Dockerfile alphafold-2.3.1/docker/Dockerfile +--- alphafold-2.3.1.orig/docker/Dockerfile 2023-03-28 10:58:07.081432000 +0200 ++++ alphafold-2.3.1/docker/Dockerfile 2023-03-28 11:04:09.608354000 +0200 +@@ -76,7 +76,6 @@ + + # Apply OpenMM patch. + WORKDIR /opt/conda/lib/python3.8/site-packages +-RUN patch -p0 < /app/alphafold/docker/openmm.patch + + # Add SETUID bit to the ldconfig binary so that non-root users can run it. + RUN chmod u+s /sbin/ldconfig.real +diff -Nru alphafold-2.3.1.orig/notebooks/AlphaFold.ipynb alphafold-2.3.1/notebooks/AlphaFold.ipynb +--- alphafold-2.3.1.orig/notebooks/AlphaFold.ipynb 2023-03-28 10:58:07.092241000 +0200 ++++ alphafold-2.3.1/notebooks/AlphaFold.ipynb 2023-03-28 11:04:51.464351000 +0200 +@@ -103,16 +103,16 @@ + " %shell rm -rf /opt/conda\n", + " %shell wget -q -P /tmp \\\n", + " https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh \\\n", +- " \u0026\u0026 bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \\\n", +- " \u0026\u0026 rm /tmp/Miniconda3-latest-Linux-x86_64.sh\n", ++ " && bash /tmp/Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda \\\n", ++ " && rm /tmp/Miniconda3-latest-Linux-x86_64.sh\n", + " pbar.update(9)\n", + "\n", + " PATH=%env PATH\n", + " %env PATH=/opt/conda/bin:{PATH}\n", + " %shell conda install -qy conda==4.13.0 \\\n", +- " \u0026\u0026 conda install -qy -c conda-forge \\\n", ++ " && conda install -qy -c conda-forge \\\n", + " python=3.8 \\\n", +- " openmm=7.5.1 \\\n", ++ " openmm=7.7.0 \\\n", + " pdbfixer\n", + " pbar.update(80)\n", + "\n", +@@ -161,8 +161,7 @@ + " pbar.update(10)\n", + "\n", + " # Apply OpenMM patch.\n", +- " %shell pushd /opt/conda/lib/python3.8/site-packages/ \u0026\u0026 \\\n", +- " patch -p0 \u003c /content/alphafold/docker/openmm.patch \u0026\u0026 \\\n", ++ " %shell pushd /opt/conda/lib/python3.8/site-packages/ && \\\n", + " popd\n", + "\n", + " # Make sure stereo_chemical_props.txt is in all locations where it could be searched for.\n", +@@ -186,9 +185,9 @@ + "\n", + "import jax\n", + "if jax.local_devices()[0].platform == 'tpu':\n", +- " raise RuntimeError('Colab TPU runtime not supported. Change it to GPU via Runtime -\u003e Change Runtime Type -\u003e Hardware accelerator -\u003e GPU.')\n", ++ " raise RuntimeError('Colab TPU runtime not supported. Change it to GPU via Runtime -> Change Runtime Type -> Hardware accelerator -> GPU.')\n", + "elif jax.local_devices()[0].platform == 'cpu':\n", +- " raise RuntimeError('Colab CPU runtime not supported. Change it to GPU via Runtime -\u003e Change Runtime Type -\u003e Hardware accelerator -\u003e GPU.')\n", ++ " raise RuntimeError('Colab CPU runtime not supported. Change it to GPU via Runtime -> Change Runtime Type -> Hardware accelerator -> GPU.')\n", + "else:\n", + " print(f'Running with {jax.local_devices()[0].device_kind} GPU')\n", + "\n", +@@ -206,7 +205,7 @@ + "source": [ + "## Making a prediction\n", + "\n", +- "Please paste the sequence of your protein in the text box below, then run the remaining cells via _Runtime_ \u003e _Run after_. You can also run the cells individually by pressing the _Play_ button on the left.\n", ++ "Please paste the sequence of your protein in the text box below, then run the remaining cells via _Runtime_ > _Run after_. You can also run the cells individually by pressing the _Play_ button on the left.\n", + "\n", + "Note that the search against databases and the actual prediction can take some time, from minutes to hours, depending on the length of the protein and what type of GPU you are allocated by Colab (see FAQ below)." + ] +@@ -298,21 +297,21 @@ + "\n", + "# Check whether total length exceeds limit.\n", + "total_sequence_length = sum([len(seq) for seq in sequences])\n", +- "if total_sequence_length \u003e MAX_LENGTH:\n", ++ "if total_sequence_length > MAX_LENGTH:\n", + " raise ValueError('The total sequence length is too long: '\n", + " f'{total_sequence_length}, while the maximum is '\n", + " f'{MAX_LENGTH}.')\n", + "\n", + "# Check whether we exceed the monomer limit.\n", + "if model_type_to_use == ModelType.MONOMER:\n", +- " if len(sequences[0]) \u003e MAX_MONOMER_MODEL_LENGTH:\n", ++ " if len(sequences[0]) > MAX_MONOMER_MODEL_LENGTH:\n", + " raise ValueError(\n", + " f'Input sequence is too long: {len(sequences[0])} amino acids, while '\n", + " f'the maximum for the monomer model is {MAX_MONOMER_MODEL_LENGTH}. You may '\n", + " 'be able to run this sequence with the multimer model by selecting the '\n", + " 'use_multimer_model_for_monomers checkbox above.')\n", + " \n", +- "if total_sequence_length \u003e MAX_VALIDATED_LENGTH:\n", ++ "if total_sequence_length > MAX_VALIDATED_LENGTH:\n", + " print('WARNING: The accuracy of the system has not been fully validated '\n", + " 'above 3000 residues, and you may experience long running times or '\n", + " f'run out of memory. Total sequence length is {total_sequence_length} '\n", +@@ -407,7 +406,7 @@ + "]\n", + "\n", + "# Search UniProt and construct the all_seq features only for heteromers, not homomers.\n", +- "if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) \u003e 1:\n", ++ "if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) > 1:\n", + " MSA_DATABASES.extend([\n", + " # Swiss-Prot and TrEMBL are concatenated together as UniProt.\n", + " {'db_name': 'uniprot',\n", +@@ -441,7 +440,7 @@ + " for sequence_index, sequence in enumerate(sorted(set(sequences)), 1):\n", + " fasta_path = f'target_{sequence_index:02d}.fasta'\n", + " with open(fasta_path, 'wt') as f:\n", +- " f.write(f'\u003equery\\n{sequence}')\n", ++ " f.write(f'>query\\n{sequence}')\n", + " sequence_to_fasta_path[sequence] = fasta_path\n", + "\n", + " # Run the search against chunks of genetic databases (since the genetic\n", +@@ -502,7 +501,7 @@ + " num_templates=0, num_res=len(sequence)))\n", + "\n", + " # Construct the all_seq features only for heteromers, not homomers.\n", +- " if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) \u003e 1:\n", ++ " if model_type_to_use == ModelType.MULTIMER and len(set(sequences)) > 1:\n", + " valid_feats = msa_pairing.MSA_FEATURES + (\n", + " 'msa_species_identifiers',\n", + " )\n", +@@ -662,7 +661,7 @@ + "banded_b_factors = []\n", + "for plddt in plddts[best_model_name]:\n", + " for idx, (min_val, max_val, _) in enumerate(PLDDT_BANDS):\n", +- " if plddt \u003e= min_val and plddt \u003c= max_val:\n", ++ " if plddt >= min_val and plddt <= max_val:\n", + " banded_b_factors.append(idx)\n", + " break\n", + "banded_b_factors = np.array(banded_b_factors)[:, None] * final_atom_mask\n", +@@ -675,14 +674,14 @@ + " f.write(relaxed_pdb)\n", + "\n", + "\n", +- "# --- Visualise the prediction \u0026 confidence ---\n", ++ "# --- Visualise the prediction & confidence ---\n", + "show_sidechains = True\n", + "def plot_plddt_legend():\n", + " \"\"\"Plots the legend for pLDDT.\"\"\"\n", +- " thresh = ['Very low (pLDDT \u003c 50)',\n", +- " 'Low (70 \u003e pLDDT \u003e 50)',\n", +- " 'Confident (90 \u003e pLDDT \u003e 70)',\n", +- " 'Very high (pLDDT \u003e 90)']\n", ++ " thresh = ['Very low (pLDDT < 50)',\n", ++ " 'Low (70 > pLDDT > 50)',\n", ++ " 'Confident (90 > pLDDT > 70)',\n", ++ " 'Very high (pLDDT > 90)']\n", + "\n", + " colors = [x[2] for x in PLDDT_BANDS]\n", + "\n", +@@ -796,13 +795,13 @@ + "id": "jeb2z8DIA4om" + }, + "source": [ +- "## FAQ \u0026 Troubleshooting\n", ++ "## FAQ & Troubleshooting\n", + "\n", + "\n", + "* How do I get a predicted protein structure for my protein?\n", + " * Click on the _Connect_ button on the top right to get started.\n", + " * Paste the amino acid sequence of your protein (without any headers) into the “Enter the amino acid sequence to fold”.\n", +- " * Run all cells in the Colab, either by running them individually (with the play button on the left side) or via _Runtime_ \u003e _Run all._ Make sure you run all 5 cells in order.\n", ++ " * Run all cells in the Colab, either by running them individually (with the play button on the left side) or via _Runtime_ > _Run all._ Make sure you run all 5 cells in order.\n", + " * The predicted protein structure will be downloaded once all cells have been executed. Note: This can take minutes to hours - see below.\n", + "* How long will this take?\n", + " * Downloading the AlphaFold source code can take up to a few minutes.\n", +@@ -811,8 +810,8 @@ + " * Running AlphaFold and generating the prediction can take minutes to hours, depending on the length of your protein and on which GPU-type Colab has assigned you.\n", + "* My Colab no longer seems to be doing anything, what should I do?\n", + " * Some steps may take minutes to hours to complete.\n", +- " * If nothing happens or if you receive an error message, try restarting your Colab runtime via _Runtime_ \u003e _Restart runtime_.\n", +- " * If this doesn’t help, try resetting your Colab runtime via _Runtime_ \u003e _Factory reset runtime_.\n", ++ " * If nothing happens or if you receive an error message, try restarting your Colab runtime via _Runtime_ > _Restart runtime_.\n", ++ " * If this doesn’t help, try resetting your Colab runtime via _Runtime_ > _Factory reset runtime_.\n", + "* How does this compare to the open-source version of AlphaFold?\n", + " * This Colab version of AlphaFold searches a selected portion of the BFD dataset and currently doesn’t use templates, so its accuracy is reduced in comparison to the full version of AlphaFold that is described in the [AlphaFold paper](https://doi.org/10.1038/s41586-021-03819-2) and [Github repo](https://github.com/deepmind/alphafold/) (the full version is available via the inference script).\n", + "* What is a Colab?\n", +@@ -821,7 +820,7 @@ + " * The resources allocated to your Colab vary. See the [Colab FAQ](https://research.google.com/colaboratory/faq.html) for more details.\n", + " * You can execute the Colab nonetheless.\n", + "* I received an error “Colab CPU runtime not supported” or “No GPU/TPU found”, what do I do?\n", +- " * Colab CPU runtime is not supported. Try changing your runtime via _Runtime_ \u003e _Change runtime type_ \u003e _Hardware accelerator_ \u003e _GPU_.\n", ++ " * Colab CPU runtime is not supported. Try changing your runtime via _Runtime_ > _Change runtime type_ > _Hardware accelerator_ > _GPU_.\n", + " * The type of GPU allocated to your Colab varies. See the [Colab FAQ](https://research.google.com/colaboratory/faq.html) for more details.\n", + " * If you receive “Cannot connect to GPU backend”, you can try again later to see if Colab allocates you a GPU.\n", + " * [Colab Pro](https://colab.research.google.com/signup) offers priority access to GPUs.\n", diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb new file mode 100644 index 000000000000..0842216c4e9f --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-CUDA-11.7.0-ColabFold.eb @@ -0,0 +1,178 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.3.4' +_colab_suffix = '-ColabFold' +_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = _cuda_suffix + _colab_suffix +_commit = '41807ea2c75706cf03f790f06ca191dc04331e41' + +homepage = 'https://github.com/sokrypton/alphafold' +description = """ +AlphaFold can predict protein structures with atomic accuracy even where no +similar structure is known. +This package of AlphaFold contains patches for ColabFold.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + # required for installing dm-tree + ('Bazel', '5.1.1'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('TensorFlow', '2.11.0', _cuda_suffix), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.5'), + ('jax', '0.3.25', _cuda_suffix), # also provides absl-py + ('UCX-CUDA', '1.12.1', _cuda_suffix), + ('cuDNN', '8.4.1.50', _cuda_suffix, SYSTEM), + ('NCCL', '2.12.12', _cuda_suffix), + ('OpenMM', '8.0.0', _cuda_suffix), +] + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/sokrypton/alphafold/archive/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': '%s.tar.gz' % _commit, + 'filename': '%s-%s.tar.gz' % (name.lower() + _colab_suffix.lower(), version) + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-ColabFold-2.3.4_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-ColabFold-2.3.4_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.3.1_use_openmm_7.7.0.patch', + ], + 'checksums': [ + 'be6778333fc110b8662b0e262798d6fc1663a14d9341469c6558b2d7771b8024', # alphafold-colabfold-2.3.4.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + # AlphaFold-ColabFold-2.3.4_data-dep-paths.patch + '3826e357c35a58b2c8c0fab41ac8ae1b4d4c135162fe47ded577a13dade0c6f3', + # AlphaFold-2.0.0_n-cpu.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', + # AlphaFold-ColabFold-2.3.4_fix-scp-path.patch + '07bf81f987bc1ab67b7d71121396449289d3ffb499cddb62a135574f2ca7115a', + # AlphaFold-2.0.1_setup_rm_tfcpu.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', + # AlphaFold-2.3.1_use_openmm_7.7.0.patch + 'd800bb085deac7edbe2d72916c1194043964aaf51b88a3b5a5016ab68a1090ec', + ], + 'start_dir': 'alphafold-%s' % _commit, + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.8.1', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('chex', '0.1.6', { + 'checksums': ['adb5d2352b5f0d248ccf594be1b1bf9ee7a2bee2a57f0eac78547538d479b0e7'], + }), + ('tabulate', '0.9.0', { + 'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('dm-tree', '0.1.8', { + 'modulename': 'tree', + 'checksums': ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'], + }), + ('websocket-client', '1.5.1', { + 'modulename': 'websocket', + 'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'], + }), + ('docker', '6.0.1', { + 'checksums': ['896c4282e5c7af5c45e8b683b0b0c33932974fe6e50fc6906a0a83616ab3da97'], + }), + ('immutabledict', '2.2.3', { + 'checksums': ['0e1e8a3f2b3ff062daa19795f947e9ec7a58add269d44e34d3ab4319e1343853'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), +] + +_alphafold_buildir = '%%(builddir)s/%%(namelower)s-%s' % _commit + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %s/run_alphafold.py >> %%(installdir)s/bin/run_alphafold.py" % _alphafold_buildir, + "chmod a+x %(installdir)s/bin/run_alphafold*.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %s/scripts %%(installdir)s/" % _alphafold_buildir, + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:$PYTHONPATH " + "python %s/run_alphafold_test.py" % _alphafold_buildir, +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m openmm.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +# these allow to make predictions on proteins that would typically be too long to fit into GPU memory; +# see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py +modextravars = { + 'TF_FORCE_UNIFIED_MEMORY': '1', + 'XLA_PYTHON_CLIENT_MEM_FRACTION': '3', + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt, + 'OPENMM_RELAX': 'CUDA' # unset or set to 'CPU' in order not to run the energy minimization on GPU; PR#189 +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb new file mode 100644 index 000000000000..614a7fe1e6ea --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-2.3.4-foss-2022a-ColabFold.eb @@ -0,0 +1,167 @@ +easyblock = 'PythonBundle' + +name = 'AlphaFold' +version = '2.3.4' +versionsuffix = '-ColabFold' +_commit = '41807ea2c75706cf03f790f06ca191dc04331e41' + +homepage = 'https://github.com/sokrypton/alphafold' +description = """ +AlphaFold can predict protein structures with atomic accuracy even where no +similar structure is known. +This package of AlphaFold contains patches for ColabFold.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + # required for installing dm-tree + ('Bazel', '5.1.1'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('TensorFlow', '2.11.0'), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.5'), + ('jax', '0.3.25'), # also provides absl-py + ('OpenMM', '8.0.0'), +] + +# commit to use for downloading stereo_chemical_props.txt and copy to alphafold/common, +# see docker/Dockerfile in AlphaFold repository +local_scp_commit = '7102c6' + +components = [ + (name, version, { + 'easyblock': 'PythonPackage', + 'source_urls': [ + 'https://github.com/sokrypton/alphafold/archive/', + 'https://git.scicore.unibas.ch/schwede/openstructure/-/raw/%s/modules/mol/alg/src/' % local_scp_commit, + ], + 'sources': [ + { + 'download_filename': '%s.tar.gz' % _commit, + 'filename': '%s-%s.tar.gz' % (name.lower() + versionsuffix.lower(), version) + }, + { + 'download_filename': 'stereo_chemical_props.txt', + 'filename': 'stereo_chemical_props-%s.txt' % local_scp_commit, + 'extract_cmd': "cp %s .", + }, + ], + 'patches': [ + 'AlphaFold-ColabFold-2.3.4_data-dep-paths.patch', + 'AlphaFold-2.0.0_n-cpu.patch', + 'AlphaFold-ColabFold-2.3.4_fix-scp-path.patch', + 'AlphaFold-2.0.1_setup_rm_tfcpu.patch', + 'AlphaFold-2.3.1_use_openmm_7.7.0.patch', + ], + 'checksums': [ + 'be6778333fc110b8662b0e262798d6fc1663a14d9341469c6558b2d7771b8024', # alphafold-colabfold-2.3.4.tar.gz + '24510899eeb49167cffedec8fa45363a4d08279c0c637a403b452f7d0ac09451', # stereo_chemical_props-7102c6.txt + # AlphaFold-ColabFold-2.3.4_data-dep-paths.patch + '3826e357c35a58b2c8c0fab41ac8ae1b4d4c135162fe47ded577a13dade0c6f3', + # AlphaFold-2.0.0_n-cpu.patch + 'dfda4dd5f9aba19fe2b6eb9a0ec583d12dcefdfee8ab8803fc57ad48d582db04', + # AlphaFold-ColabFold-2.3.4_fix-scp-path.patch + '07bf81f987bc1ab67b7d71121396449289d3ffb499cddb62a135574f2ca7115a', + # AlphaFold-2.0.1_setup_rm_tfcpu.patch + '1a2e4e843bd9a4d15ee39e6c37cc63ba281311cc7a0a5610f0e43b52ef93faac', + # AlphaFold-2.3.1_use_openmm_7.7.0.patch + 'd800bb085deac7edbe2d72916c1194043964aaf51b88a3b5a5016ab68a1090ec', + ], + 'start_dir': 'alphafold-%s' % _commit, + 'use_pip': True, + }), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.8.1', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d50551abfe9dbaefc066f4d9d400cdebe57f1fefd9de9d01e12beb87efd99595'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('chex', '0.1.6', { + 'checksums': ['adb5d2352b5f0d248ccf594be1b1bf9ee7a2bee2a57f0eac78547538d479b0e7'], + }), + ('tabulate', '0.9.0', { + 'checksums': ['0095b12bf5966de529c0feb1fa08671671b3368eec77d7ef7ab114be2c068b3c'], + }), + ('jmp', '0.0.4', { + 'checksums': ['5dfeb0fd7c7a9f72a70fff0aab9d0cbfae32a809c02f4037ff3485ceb33e1730'], + }), + ('dm-haiku', '0.0.9', { + 'modulename': 'haiku', + 'source_urls': ['https://github.com/deepmind/dm-haiku/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d550f07f5891ede30ada5faafde98f549ed1b8ceadb7a601cca3d81db7d82414'], + }), + ('dm-tree', '0.1.8', { + 'modulename': 'tree', + 'checksums': ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'], + }), + ('websocket-client', '1.5.1', { + 'modulename': 'websocket', + 'checksums': ['3f09e6d8230892547132177f575a4e3e73cfdf06526e20cc02aa1c3b47184d40'], + }), + ('docker', '6.0.1', { + 'checksums': ['896c4282e5c7af5c45e8b683b0b0c33932974fe6e50fc6906a0a83616ab3da97'], + }), + ('immutabledict', '2.2.3', { + 'checksums': ['0e1e8a3f2b3ff062daa19795f947e9ec7a58add269d44e34d3ab4319e1343853'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), +] + +_alphafold_buildir = '%%(builddir)s/%%(namelower)s-%s' % _commit + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + # run_alphafold.py script is missing a shebang... + "echo '#!/usr/bin/env python' > %(installdir)s/bin/run_alphafold.py", + "cat %s/run_alphafold.py >> %%(installdir)s/bin/run_alphafold.py" % _alphafold_buildir, + "chmod a+x %(installdir)s/bin/run_alphafold*.py", + "cd %(installdir)s/bin && ln -s run_alphafold.py alphafold", + "cp -a %s/scripts %%(installdir)s/" % _alphafold_buildir, + "cp %%(builddir)s/stereo_chemical_props-%s.txt %%(installdir)s/stereo_chemical_props.txt" % local_scp_commit, + # run tests for run_alphafold.py script; + # shouldn't do this in sanity check to avoid breaking use of --module-only + "PYTHONPATH=%%(installdir)s/lib/python%%(pyshortver)s/site-packages:$PYTHONPATH " + "python %s/run_alphafold_test.py" % _alphafold_buildir, +] + +sanity_check_paths = { + 'files': ['bin/alphafold', 'bin/pdbfixer', 'bin/run_alphafold.py', 'stereo_chemical_props.txt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'scripts'], +} + +sanity_check_commands = [ + "pdbfixer --help", + "python -m openmm.testInstallation", + "python -c 'import alphafold'", + "alphafold --help 2>&1 | grep 'Full AlphaFold protein structure prediction script'", +] + +sanity_pip_check = True + +modextravars = { + # 'ALPHAFOLD_DATA_DIR': '/path/to/AlphaFold_DBs', # please adapt +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_data-dep-paths.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_data-dep-paths.patch new file mode 100644 index 000000000000..388d7aa02d2c --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_data-dep-paths.patch @@ -0,0 +1,134 @@ +pick up on $ALPHAFOLD_DATA_DIR to specify location to downloaded data +(see https://github.com/deepmind/alphafold/blob/main/docker/run_docker.py); +pick up on HH-suite, HHMER, Kalign dependencies provided via EasyBuild +author: Kenneth Hoste (HPC-UGent) +--- run_alphafold.py.orig 2023-02-18 15:59:05.000000000 +0100 ++++ run_alphafold.py 2023-04-17 13:54:08.910029182 +0200 +@@ -42,6 +42,46 @@ + import numpy as np + + # Internal import (7716). ++use_reduced_dbs = any("--db_preset=reduced_dbs" in s for s in sys.argv[1:]) ++use_monomer_preset = not any("--model_preset=multimer" in s for s in sys.argv[1:]) ++ ++data_dir = os.getenv('ALPHAFOLD_DATA_DIR') ++use_gpu_relax = os.getenv('OPENMM_RELAX')=='CUDA' ++ ++if data_dir: ++ mgnify_database_path = os.path.join(data_dir, 'mgnify', 'mgy_clusters_2022_05.fa') ++ uniref90_database_path = os.path.join(data_dir, 'uniref90', 'uniref90.fasta') ++ template_mmcif_dir = os.path.join(data_dir, 'pdb_mmcif', 'mmcif_files') ++ obsolete_pdbs_path = os.path.join(data_dir, 'pdb_mmcif', 'obsolete.dat') ++ if use_monomer_preset: ++ pdb_seqres_database_path = None ++ uniprot_database_path = None ++ pdb70_database_path = os.path.join(data_dir, 'pdb70', 'pdb70') ++ else: ++ pdb_seqres_database_path = os.path.join(data_dir, 'pdb_seqres', 'pdb_seqres.txt') ++ uniprot_database_path = os.path.join(data_dir, 'uniprot', 'uniprot.fasta') ++ pdb70_database_path = None ++ if use_reduced_dbs: ++ small_bfd_database_path = os.path.join(data_dir, 'small_bfd','bfd-first_non_consensus_sequences.fasta') ++ uniref30_database_path = None ++ bfd_database_path = None ++ else: ++ small_bfd_database_path = None ++ bfd_database_path = os.path.join(data_dir, 'bfd', 'bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt') ++ uniref30_database_path = os.path.join(data_dir, 'uniref30', 'UniRef30_2021_03') ++else: ++ sys.stderr.write("$ALPHAFOLD_DATA_DIR is not defined!") ++ uniref90_database_path = None ++ mgnify_database_path = None ++ bfd_database_path = None ++ uniref30_database_path = None ++ pdb70_database_path = None ++ template_mmcif_dir = None ++ obsolete_pdbs_path = None ++ small_bfd_database_path = None ++ uniprot_database_path = None ++ pdb_seqres_database_path = None ++ use_gpu_relax = None + + logging.set_verbosity(logging.INFO) + +@@ -59,7 +99,7 @@ + 'separated by commas. All FASTA paths must have a unique basename as the ' + 'basename is used to name the output directories for each prediction.') + +-flags.DEFINE_string('data_dir', None, 'Path to directory of supporting data.') ++flags.DEFINE_string('data_dir', data_dir, 'Path to directory of supporting data.') + flags.DEFINE_string('output_dir', None, 'Path to a directory that will ' + 'store the results.') + flags.DEFINE_string('jackhmmer_binary_path', shutil.which('jackhmmer'), +@@ -74,27 +114,27 @@ + 'Path to the hmmbuild executable.') + flags.DEFINE_string('kalign_binary_path', shutil.which('kalign'), + 'Path to the Kalign executable.') +-flags.DEFINE_string('uniref90_database_path', None, 'Path to the Uniref90 ' ++flags.DEFINE_string('uniref90_database_path', uniref90_database_path, 'Path to the Uniref90 ' + 'database for use by JackHMMER.') +-flags.DEFINE_string('mgnify_database_path', None, 'Path to the MGnify ' ++flags.DEFINE_string('mgnify_database_path', mgnify_database_path, 'Path to the MGnify ' + 'database for use by JackHMMER.') +-flags.DEFINE_string('bfd_database_path', None, 'Path to the BFD ' ++flags.DEFINE_string('bfd_database_path', bfd_database_path, 'Path to the BFD ' + 'database for use by HHblits.') +-flags.DEFINE_string('small_bfd_database_path', None, 'Path to the small ' ++flags.DEFINE_string('small_bfd_database_path', small_bfd_database_path, 'Path to the small ' + 'version of BFD used with the "reduced_dbs" preset.') +-flags.DEFINE_string('uniref30_database_path', None, 'Path to the UniRef30 ' ++flags.DEFINE_string('uniref30_database_path', uniref30_database_path, 'Path to the UniRef30 ' + 'database for use by HHblits.') +-flags.DEFINE_string('uniprot_database_path', None, 'Path to the Uniprot ' ++flags.DEFINE_string('uniprot_database_path', uniprot_database_path, 'Path to the Uniprot ' + 'database for use by JackHMMer.') +-flags.DEFINE_string('pdb70_database_path', None, 'Path to the PDB70 ' ++flags.DEFINE_string('pdb70_database_path', pdb70_database_path, 'Path to the PDB70 ' + 'database for use by HHsearch.') +-flags.DEFINE_string('pdb_seqres_database_path', None, 'Path to the PDB ' ++flags.DEFINE_string('pdb_seqres_database_path', pdb_seqres_database_path, 'Path to the PDB ' + 'seqres database for use by hmmsearch.') +-flags.DEFINE_string('template_mmcif_dir', None, 'Path to a directory with ' ++flags.DEFINE_string('template_mmcif_dir', template_mmcif_dir, 'Path to a directory with ' + 'template mmCIF structures, each named .cif') + flags.DEFINE_string('max_template_date', None, 'Maximum template release date ' + 'to consider. Important if folding historical test sets.') +-flags.DEFINE_string('obsolete_pdbs_path', None, 'Path to file containing a ' ++flags.DEFINE_string('obsolete_pdbs_path', obsolete_pdbs_path, 'Path to file containing a ' + 'mapping from obsolete PDB IDs to the PDB IDs of their ' + 'replacements.') + flags.DEFINE_enum('db_preset', 'full_dbs', +@@ -137,7 +177,7 @@ + 'distracting stereochemical violations but might help ' + 'in case you are having issues with the relaxation ' + 'stage.') +-flags.DEFINE_boolean('use_gpu_relax', None, 'Whether to relax on GPU. ' ++flags.DEFINE_boolean('use_gpu_relax', use_gpu_relax, 'Whether to relax on GPU. ' + 'Relax on GPU can be much faster than CPU, so it is ' + 'recommended to enable if possible. GPUs must be available' + ' if this setting is enabled.') +@@ -334,6 +374,10 @@ + 'sure it is installed on your system.') + + use_small_bfd = FLAGS.db_preset == 'reduced_dbs' ++ if use_small_bfd and data_dir: ++ bfd_database_path = None ++ uniref30_database_path = None ++ + _check_flag('small_bfd_database_path', 'db_preset', + should_be_set=use_small_bfd) + _check_flag('bfd_database_path', 'db_preset', +@@ -456,13 +500,7 @@ + flags.mark_flags_as_required([ + 'fasta_paths', + 'output_dir', +- 'data_dir', +- 'uniref90_database_path', +- 'mgnify_database_path', +- 'template_mmcif_dir', + 'max_template_date', +- 'obsolete_pdbs_path', +- 'use_gpu_relax', + ]) + + app.run(main) diff --git a/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_fix-scp-path.patch b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_fix-scp-path.patch new file mode 100644 index 000000000000..0714243785e9 --- /dev/null +++ b/easybuild/easyconfigs/a/AlphaFold/AlphaFold-ColabFold-2.3.4_fix-scp-path.patch @@ -0,0 +1,14 @@ +fix path to stereo_chemical_props.txt when AlphaFold is installed with EasyBuild +author: Kenneth Hoste (HPC-UGent) +update 2.0.0 -> 2.1.0: Thomas Hoffmann (EMBL Heidelberg) +--- alphafold/common/residue_constants.py.orig 2023-04-17 13:59:57.535153646 +0200 ++++ alphafold/common/residue_constants.py 2023-04-17 14:02:33.555747657 +0200 +@@ -25,7 +25,7 @@ + # Internal import (35fd). + + from . import __file__ +-stereo_chemical_props_path = os.path.join(os.path.dirname(__file__), f'stereo_chemical_props.txt') ++stereo_chemical_props_path = os.path.join(os.getenv('EBROOTALPHAFOLD', 'alphafold/common'), 'stereo_chemical_props.txt') + + # Distance from one CA to next CA [trans configuration: omega = 180]. + ca_ca = 3.80209737096 diff --git a/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a.eb b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a.eb new file mode 100644 index 000000000000..7efa2268907f --- /dev/null +++ b/easybuild/easyconfigs/a/Annocript/Annocript-2.0-foss-2022a.eb @@ -0,0 +1,76 @@ +easyblock = 'PackedBinary' + +name = 'Annocript' +version = '2.0' +local_commit = '84fd67b' + +homepage = 'https://github.com/frankMusacchia/Annocript' +description = """ Annocript is a pipeline for the annotation of de-novo generated transcriptomes. + It executes blast analysis with UniProt, NCBI Conserved Domain Database and Nucleotide division + adding also annotations from Gene Ontology, the Enzyme Commission and UniPathways. + Annocript also gives information about the longest ORF and the non-coding potential using external software. + Annocript is also capable to identify putative long non-coding RNAs by using an heuristic based on homology + and sequence features. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/frankMusacchia/Annocript/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +patches = [ + 'annocript_fix_paths.patch', + 'annocript_no_background.patch', +] +checksums = [ + {'Annocript-2.0.tar.gz': '151dec3a390826fd2bcc7d794a9565535702dfc9c4672842e825a9fcf21406d9'}, + {'annocript_fix_paths.patch': '95359e335a6a992f5f269e8f199c9df92d765f7ff41890298acead12d562685c'}, + {'annocript_no_background.patch': 'ca02c2b02b7574c25128c9a4ce2b69a13a0bb2b409efd2ea63562053bf2e2c57'}, +] + +dependencies = [ + ('Compress-Raw-Zlib', '2.202'), + ('Python', '3.10.4'), + ('Perl', '5.34.1'), + ('BioPerl', '1.7.8'), + ('R', '4.2.1'), + ('CPC2', '1.0.1'), + ('BLAST+', '2.13.0'), + ('LIBSVM', '3.30'), + ('MariaDB', '10.9.3'), + ('DBD-mysql', '4.050'), +] + +postinstallcmds = [ + # Extract dna2pep to annocript's bin folder, set permissions. + # It is just a series Python scripts and I'm not building it as a standalone dependency, as sources for this SW + # are not available elsewhere than in the Annocript repository anyway. + "mkdir %(installdir)s/bin ", + "cp %(builddir)s/Annocript-*/DL_PROGRAMS/dna2pep-1.1.tar.gz %(installdir)s/bin ", + "cd %(installdir)s/bin && tar -zxvf dna2pep-1.1.tar.gz ", + "rm %(installdir)s/bin/dna2pep-1.1.tar.gz && chmod 755 %(installdir)s/bin/dna2pep-1.1/dna2pep.py ", + # extract annocript itself + 'mv %(installdir)s/annocript.pl %(installdir)s/bin/', + 'sed -i -e "1s|#!.*$|#!/usr/bin/env perl|g" %(installdir)s/bin/annocript.pl', + 'chmod a+rx %(installdir)s/bin/annocript.pl', +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('CGI', '4.43', { + 'source_tmpl': 'CGI-4.43.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEEJO/'], + 'checksums': ['14b94f9df6e48fc26ebc4fa1e01a7b534cbc1611028a49028f9ac9d8ca27b734'], + }), +] + +modextrapaths = {'PERL5LIB': ['', 'lib/perl5/site_perl/%(perlver)s/']} + +sanity_check_paths = { + 'files': ['bin/annocript.pl'], + 'dirs': [], +} + +sanity_check_commands = ['annocript.pl --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/Annocript/annocript_fix_paths.patch b/easybuild/easyconfigs/a/Annocript/annocript_fix_paths.patch new file mode 100644 index 000000000000..c863a8425a1e --- /dev/null +++ b/easybuild/easyconfigs/a/Annocript/annocript_fix_paths.patch @@ -0,0 +1,36 @@ +Do not use full paths for executables in the config file: they should be in the PATH +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +diff -ruN Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/CONFIGURATION/config_user.txt Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/CONFIGURATION/config_user.txt +--- Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/CONFIGURATION/config_user.txt 2023-05-15 18:02:35.946010508 +0200 ++++ Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/CONFIGURATION/config_user.txt 2023-05-15 18:04:08.262818993 +0200 +@@ -114,7 +114,7 @@ + + #Programs Paths + diamondPath = +-blastPath = /home/francesco/bin/ncbi-blast-2.7.1+/bin/ +-lncRNAPredProgPath = /home/francesco/bin/CPC2-beta/bin/CPC2.py +-dna2pepPath = /home/francesco/bin/dna2pep-1.1/dna2pep.py ++blastPath = ++lncRNAPredProgPath = CPC2.py ++dna2pepPath = dna2pep.py + ############################## +diff -ruN Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/LIB/annocript_management.pm Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/LIB/annocript_management.pm +--- Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/LIB/annocript_management.pm 2023-05-15 18:02:36.477018945 +0200 ++++ Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/LIB/annocript_management.pm 2023-05-15 18:05:42.646383000 +0200 +@@ -748,9 +748,15 @@ + + #Here we collect the path to the programs using an array initialized in the beginning of the page + # with all the programs used by Annocript ++ # first expand executables to full path ++ use File::Which; + foreach my $program (@$blastProgramsInUse){ + my $var= $program.'Path'; +- $configHash->{$var} = $configHash->{'blastPath'}.$program; ++ $configHash->{$var} = which($program) or die "error: blast executable $program not found\n"; ++ } ++ foreach my $mypath ('lncRNAPredProgPath', 'dna2pepPath', 'makeblastdbPath'){ ++ my $myexec = $configHash->{$mypath}; ++ $configHash->{$mypath} = which($myexec) or die "error: executable $myexec not found\n"; + } + + #CONTROLS THE PATH TO THE PROGRAMS diff --git a/easybuild/easyconfigs/a/Annocript/annocript_no_background.patch b/easybuild/easyconfigs/a/Annocript/annocript_no_background.patch new file mode 100644 index 000000000000..cf3b8ef36e3d --- /dev/null +++ b/easybuild/easyconfigs/a/Annocript/annocript_no_background.patch @@ -0,0 +1,23 @@ +Do not start perl script in background +Author: Samuel Moors, Vrije Universiteit Brussel (VUB) +diff -ruN Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/annocript.pl Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/annocript.pl +--- Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9_orig/annocript.pl 2023-05-15 18:02:36.827824452 +0200 ++++ Annocript-84fd67b30b7edb0eedc4eafd0a3fad3a117055d9/annocript.pl 2023-05-15 18:13:45.525029000 +0200 +@@ -301,7 +301,7 @@ + ."\n\nPlease let us know if any problem occurs during the computation or you don't get from Annocript the expected result.\n" + ."You may want to use the forum at: https://groups.google.com/forum/#!forum/annocript.\n",$log_file);#DEBUGCODE + +- nice_printing("STARTING ANNOCRIPT IN BACKGROUND! BYE!",$log_file); ++ nice_printing("STARTING ANNOCRIPT IN FOREGROUND! BYE!",$log_file); + + close ( $logFHandle ); + +@@ -325,7 +325,7 @@ + chdir $program_folder; + + #This perl script will be run in background +- my $runAnnocriptCmd = "nohup perl ".$configHash->{'ProgExecFolder'} ."/annocript_executor.pl $user_config $program_config $timesFile $configHashPath >> $log_file &"; ++ my $runAnnocriptCmd = "perl ".$configHash->{'ProgExecFolder'} ."/annocript_executor.pl $user_config $program_config $timesFile $configHashPath >> $log_file"; + ( system($runAnnocriptCmd) ) == 0 + or die("Unable to start annocript_executor!\n"); + } diff --git a/easybuild/easyconfigs/a/Arb/Arb-2.22.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/Arb/Arb-2.22.1-foss-2021b.eb similarity index 94% rename from easybuild/easyconfigs/a/Arb/Arb-2.22.1-GCC-11.2.0.eb rename to easybuild/easyconfigs/a/Arb/Arb-2.22.1-foss-2021b.eb index f729c96081da..6aede555b93a 100644 --- a/easybuild/easyconfigs/a/Arb/Arb-2.22.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/a/Arb/Arb-2.22.1-foss-2021b.eb @@ -9,7 +9,7 @@ description = """Arb is a C library for arbitrary-precision interval arithmetic. It has full support for both real and complex numbers. The library is thread-safe, portable, and extensively tested.""" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'foss', 'version': '2021b'} toolchainopts = {'pic': True} github_account = 'fredrik-johansson' @@ -18,9 +18,9 @@ sources = ['%(version)s.tar.gz'] checksums = ['1ef85518eee04885e8a90196498bc75e4e2410621d4184f2bc01d46b7080a243'] dependencies = [ - ('FLINT', '2.8.4'), ('GMP', '6.2.1'), ('MPFR', '4.1.0'), + ('FLINT', '2.8.4'), ] configopts = '--with-flint=$EBROOTFLINT --with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR' diff --git a/easybuild/easyconfigs/a/Arb/Arb-2.23.0-gfbf-2022a.eb b/easybuild/easyconfigs/a/Arb/Arb-2.23.0-gfbf-2022a.eb new file mode 100644 index 000000000000..06c0fa3ab760 --- /dev/null +++ b/easybuild/easyconfigs/a/Arb/Arb-2.23.0-gfbf-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Arb' +version = '2.23.0' + +homepage = 'https://arblib.org/' + +description = """Arb is a C library for arbitrary-precision interval arithmetic. + It has full support for both real and complex numbers. The library is thread-safe, + portable, and extensively tested.""" + +toolchain = {'name': 'gfbf', 'version': '2022a'} +toolchainopts = {'pic': True} + +github_account = 'fredrik-johansson' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['977d41bde46f5442511d5165c705cec32c03e852c84d7d1836135d412ce702bb'] + +dependencies = [ + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('FLINT', '2.9.0'), +] + +configopts = '--with-flint=$EBROOTFLINT --with-gmp=$EBROOTGMP --with-mpfr=$EBROOTMPFR' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT, 'lib/lib%(namelower)s.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb new file mode 100644 index 000000000000..261ecca60bb2 --- /dev/null +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-11.4.3-foss-2022a.eb @@ -0,0 +1,22 @@ +name = 'Armadillo' +version = '11.4.3' + +homepage = 'https://arma.sourceforge.net/' +description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards + a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, + as well as a subset of trigonometric and statistics functions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://sourceforge.net/projects/arma/files'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['87603263664988af41da2ca4f36205e36ea47a9281fa6cfd463115f3797a1da2'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Boost', '1.79.0'), + ('arpack-ng', '3.8.0'), +] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb new file mode 100644 index 000000000000..d35cad0f1b32 --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb @@ -0,0 +1,73 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '11.0.0' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] +sources = ['apache-arrow-%(version)s.tar.gz'] +checksums = ['2dd8f0ea0848a58785628ee3a57675548d509e17213a2f5d72b0d900b43f5430'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Autotools', '20220317'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '1.9.3'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), # for numpy + ('Boost', '1.81.0'), + ('lz4', '1.9.4'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.2'), + ('snappy', '1.1.9'), + ('RapidJSON', '1.1.0'), + ('RE2', '2023-03-01'), + ('utf8proc', '2.8.0'), +] + +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/developers/python.html +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " +configopts += "-DZSTD_ROOT=$EBROOTZSTD " + +# also install Python bindings +local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_install_pyarrow_cmds += "export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s && " +local_install_pyarrow_cmds += "export Parquet_DIR=%(installdir)s && " +local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " +local_install_pyarrow_cmds += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +postinstallcmds = [local_install_pyarrow_cmds] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/python%%(pyshortver)s/site-packages/pyarrow/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/Arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", + "python -c 'import pyarrow.parquet'", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.8.0-foss-2022a.eb b/easybuild/easyconfigs/a/anndata/anndata-0.8.0-foss-2022a.eb new file mode 100644 index 000000000000..38ef7f588ea4 --- /dev/null +++ b/easybuild/easyconfigs/a/anndata/anndata-0.8.0-foss-2022a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'anndata' +version = '0.8.0' + +homepage = 'https://github.com/scverse/anndata' +description = """anndata is a Python package for handling annotated data matrices in memory and on disk, + positioned between pandas and xarray""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), +] + +use_pip = True + +exts_list = [ + ('natsort', '8.3.1', { + 'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'], + }), + (name, version, { + 'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/natsort'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["natsort --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..896c62218854 --- /dev/null +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'argtable' +version = '2.13' + +homepage = 'http://argtable.sourceforge.net/' +description = """ Argtable is an ANSI C library for parsing GNU style + command line options with a minimum of fuss. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%s%s.tar.gz' % (name, version.replace('.', '-'))] +checksums = ['8f77e8a7ced5301af6e22f47302fdbc3b1ff41f2b83c43c77ae5ca041771ddbf'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['include/argtable2.h', 'lib/libargtable2.%s' % SHLIB_EXT, 'lib/libargtable2.a'], + 'dirs': ['share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/arrow-R/arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb new file mode 100644 index 000000000000..dfe97712e3bf --- /dev/null +++ b/easybuild/easyconfigs/a/arrow-R/arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb @@ -0,0 +1,34 @@ +easyblock = 'RPackage' + +name = 'arrow-R' +version = '11.0.0.3' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/arrow' +description = "R interface to the Apache Arrow C++ library" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/arrow', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['arrow_%(version)s.tar.gz'] +checksums = ['eb939471f5f4218e6cfd62f58ccd2a0a5283d4a19a2902741c7fb25e2f016eaf'] + +dependencies = [ + ('R', '4.2.2'), + ('Arrow', '11.0.0'), +] + +preinstallopts = "export LIBARROW_BINARY=true && " + +sanity_check_paths = { + 'files': [], + 'dirs': ['arrow'], +} + +options = {'modulename': 'arrow'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb new file mode 100644 index 000000000000..879b5774c38f --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-foss-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'astropy' +version = '4.2.1' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyerfa', '1.7.3', { + 'modulename': 'erfa', + 'checksums': ['6cf3a645d63e0c575a357797903eac5d2c6591d7cdb89217c8c4d39777cf18cb'], + }), + ('extension-helpers', '0.1', { + 'checksums': ['ac8a6fe91c6d98986a51a9f08ca0c7945f8fd70d95b662ced4040ae5eb973882'], + }), + (name, version, { + 'checksums': ['ed483e472241153daec45f4b0c318c2c63d9f47305b78e6e63d32fc388c18427'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/astropy'], +} + +moduleclass = 'astro' diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb new file mode 100644 index 000000000000..878eb8ce9fb7 --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-4.2.1-intel-2020b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'astropy' +version = '4.2.1' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'intel', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyerfa', '1.7.3', { + 'modulename': 'erfa', + 'checksums': ['6cf3a645d63e0c575a357797903eac5d2c6591d7cdb89217c8c4d39777cf18cb'], + }), + ('extension-helpers', '0.1', { + 'checksums': ['ac8a6fe91c6d98986a51a9f08ca0c7945f8fd70d95b662ced4040ae5eb973882'], + }), + (name, version, { + 'checksums': ['ed483e472241153daec45f4b0c318c2c63d9f47305b78e6e63d32fc388c18427'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/astropy'], +} + +moduleclass = 'astro' diff --git a/easybuild/easyconfigs/a/astropy/astropy-5.2.2-gfbf-2022b.eb b/easybuild/easyconfigs/a/astropy/astropy-5.2.2-gfbf-2022b.eb new file mode 100644 index 000000000000..16a331513362 --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-5.2.2-gfbf-2022b.eb @@ -0,0 +1,37 @@ +easyblock = "PythonBundle" + +name = 'astropy' +version = '5.2.2' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop a common +core package for Astronomy in Python and foster an ecosystem of interoperable +astronomy packages. + +The Astropy community is committed to supporting diversity and inclusion.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('PyYAML', '6.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyerfa', '2.0.0.3', { + 'modulename': 'erfa', + 'checksums': ['d77fbbfa58350c194ccb99e5d93aa05d3c2b14d5aad8b662d93c6ad9fff41f39'], + }), + ('extension-helpers', '1.0.0', { + 'checksums': ['ca1bfac67c79cf4a7a0c09286ce2a24eec31bf17715818d0726318dd0e5050e6'], + }), + (name, version, { + 'checksums': ['e6a9e34716bda5945788353c63f0644721ee7e5447d16b1cdcb58c48a96b0d9c'], + }), +] + +moduleclass = 'astro' diff --git a/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb b/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb new file mode 100644 index 000000000000..8ef5d09f68e8 --- /dev/null +++ b/easybuild/easyconfigs/a/avro-cpp/avro-cpp-1.11.1-GCC-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'avro-cpp' +version = '1.11.1' + +homepage = 'https://avro.apache.org' +description = """C++ implementation of Avro data serialization system.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/apache/avro/archive/refs/tags/'] +sources = ['release-%(version)s.tar.gz'] +checksums = ['599f96bb405f72a35154b2477caa6254d723bb4e3f6a0e54e9ae540664321752'] + +builddependencies = [ + ('CMake', '3.22.1'), +] +dependencies = [ + ('Boost', '1.77.0'), +] + +srcdir = "lang/c++" + +generator = "Unix Makefiles" +separate_build_dir = True + +sanity_check_paths = { + 'files': ["bin/avrogencpp"], + 'dirs': ["lib"], +} + +sanity_check_commands = ["avrogencpp -h"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/awscli/awscli-2.11.21-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/awscli/awscli-2.11.21-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..080aebf98557 --- /dev/null +++ b/easybuild/easyconfigs/a/awscli/awscli-2.11.21-GCCcore-11.3.0.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonBundle' + +name = 'awscli' +version = '2.11.21' + +homepage = 'https://pypi.python.org/pypi/awscli' +description = 'Universal Command Line Environment for AWS' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), # required for awscrt +] + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('ruamel.yaml', '0.17.21'), +] + +use_pip = True + +exts_list = [ + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('botocore', '1.29.138', { + 'checksums': ['31edc237088c104f7a05887646bbec31d7459dd2e108fd90cbffa315902817e2'], + }), + ('s3transfer', '0.6.1', { + 'checksums': ['640bb492711f4c0c0905e1f62b6aaeb771881935ad27884852411f8e9cacbca9'], + }), + ('prompt-toolkit', '3.0.38', { + 'sources': ['prompt_toolkit-%(version)s.tar.gz'], + 'checksums': ['23ac5d50538a9a38c8bde05fecb47d0b403ecd0662857a86f886f798563d5b9b'], + }), + ('distro', '1.8.0', { + 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + }), + ('awscrt', '0.16.16', { + 'checksums': ['13075df2c1d7942fe22327b6483274517ee0f6ae765c4e6b6ae9ef5b4c43a827'], + # cfr. https://github.com/awslabs/aws-crt-python/tree/main#openssl-and-libcrypto-unix-only + 'preinstallopts': "export AWS_CRT_BUILD_USE_SYSTEM_LIBCRYPTO=1 && ", + }), + (name, version, { + 'source_urls': ['https://github.com/aws/aws-cli/archive/'], + 'source_tmpl': '%(version)s.tar.gz', + 'checksums': ['74b6f7b1d773eafdefbb0972ea8db68be6814d382d7406707e94a25a0e6c1ebf'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/aws'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ["aws help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb new file mode 100644 index 000000000000..9fe5174b2871 --- /dev/null +++ b/easybuild/easyconfigs/b/BAMM/BAMM-2.5.0-foss-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'BAMM' +version = '2.5.0' + +homepage = 'http://bamm-project.org/' +description = """ BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. +It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of +lineage diversification and trait evolution. """ + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +# https://github.com/macroevolution/bamm +github_account = 'macroevolution' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['526eef85ef011780ee21fe65cbc10ecc62efe54044102ae40bdef49c2985b4f4'] + +builddependencies = [('CMake', '3.23.1')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} +sanity_check_commands = ["%(namelower)s"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-12.2.0.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-12.2.0.eb new file mode 100644 index 000000000000..e85979fa0335 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.30.0-GCC-12.2.0.eb @@ -0,0 +1,45 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.30.0' + +homepage = "https://bedtools.readthedocs.io/" +description = """BEDTools: a powerful toolset for genome arithmetic. +The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and +computing coverage. +The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['333ad1ffcdc6e36005b4d6c9290677986ee97871cff92ed821c1b643d38150b8'] + +builddependencies = [('Python', '3.10.8')] + +dependencies = [ + ('XZ', '5.2.7'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('BamTools', '2.5.2'), +] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +sanity_check_commands = ['bedtools --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb index 1e4df1d96356..f6a9bc03101b 100644 --- a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb +++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2022a.eb @@ -12,7 +12,11 @@ toolchain = {'name': 'foss', 'version': '2022a'} source_urls = ['https://github.com/Gaius-Augustus/BRAKER/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['eef3c4037364472988a010322cbd79b5171158f9c016f4383809adade4866c06'] +patches = ['BRAKER-%(version)s_fix-incorrect-ids.patch'] +checksums = [ + {'v2.1.6.tar.gz': 'eef3c4037364472988a010322cbd79b5171158f9c016f4383809adade4866c06'}, + {'BRAKER-2.1.6_fix-incorrect-ids.patch': '2b219de070d109637a2660a456a1f9ced48c58197385e3b3924ae90c84b41d41'}, +] dependencies = [ ('Perl', '5.34.1'), @@ -25,6 +29,8 @@ dependencies = [ ('Exonerate', '2.4.0'), ('BLAST+', '2.13.0'), ('Biopython', '1.79'), + ('DIAMOND', '2.1.0'), + ('CDBtools', '0.99'), ] fix_perl_shebang_for = ['scripts/*.pl'] diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6_fix-incorrect-ids.patch b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6_fix-incorrect-ids.patch new file mode 100644 index 000000000000..3c9df7a402df --- /dev/null +++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6_fix-incorrect-ids.patch @@ -0,0 +1,44 @@ +From f38630c1cad3e11b525f84d517c7949cb4c2d7eb Mon Sep 17 00:00:00 2001 +From: Katharina Hoff +Date: Mon, 19 Apr 2021 16:34:57 +0200 +Subject: [PATCH] fixing part of the issue + https://github.com/Gaius-Augustus/BRAKER/issues/354 where gene and transcript + line have incorrect ids + +--- + scripts/merge_transcript_sets.pl | 8 ++++---- + 1 file changed, 4 insertions(+), 4 deletions(-) + +diff --git a/scripts/merge_transcript_sets.pl b/scripts/merge_transcript_sets.pl +index 04f6c3e..5cfd6c0 100755 +--- a/scripts/merge_transcript_sets.pl ++++ b/scripts/merge_transcript_sets.pl +@@ -83,14 +83,15 @@ + my $txid; + if($line =~ m/transcript_id/){ + $line =~ m/transcript_id "([^"]+)";/; ++ + $txid = $1; + push(@{$txid_to_elements{$txid}}, $line); + foreach(@store_for_txid){ +- push(@{$txid_to_elements{$txid}}, $_) ++ push(@{$txid_to_elements{$txid}}, $_); + } + @store_for_txid = (); + }else{ +- $line =~ s/\t([\t]+)$/\tfile_${file_counter}_$1/; ++ $line =~ s/\t([^\t]+)$/\tfile_${file_counter}_$1/; + push(@store_for_txid, $line); + } + # currently, UTR features are ignored +@@ -111,9 +112,8 @@ + # always keep the first occuring transcript structure, only add from other gene sets if it has not been in the set, yet + # this might discard alternative UTR splicing isoforms at present + while (my ($key, $value) = each (%txid_to_struct_local)){ +- #print "key is $key and value is $value\n"; ++ print "key is $key and value is $value\n"; + if(not(defined($uniq_struct_to_txid{$value}))){ +- #print "adding transcript\n"; + $uniq_struct_to_txid{$value} = $key; + } + } diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..ec08bbe74b10 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-12.2.0.eb @@ -0,0 +1,50 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.17' + +homepage = 'http://bio-bwa.sourceforge.net/' + +description = """ + Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively + short nucleotide sequences against a long reference sequence such as the human + genome. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Perl', '5.36.0'), + ('zlib', '1.2.12'), +] + +# Allow use of x86 intrinsics on PPC +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' +prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && " +prebuildopts += "sed -i 's|^CFLAGS=|#CFLAGS=|g' Makefile && " +prebuildopts += "sed -i 's|^LIBS=|LIBS= $(LDFLAGS) |g' Makefile && " + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-12.2.0.eb b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-12.2.0.eb new file mode 100644 index 000000000000..324af5c529f3 --- /dev/null +++ b/easybuild/easyconfigs/b/BamTools/BamTools-2.5.2-GCC-12.2.0.eb @@ -0,0 +1,19 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +name = 'BamTools' +version = '2.5.2' + +homepage = 'https://github.com/pezmaster31/bamtools' +description = "BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files." + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +# https://github.com/pezmaster31/bamtools +github_account = 'pezmaster31' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4d8b84bd07b673d0ed41031348f10ca98dd6fa6a4460f9b9668d6f1d4084dfc8'] + +builddependencies = [('CMake', '3.24.3')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb new file mode 100644 index 000000000000..840b2a8d6faa --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Bio-SearchIO-hmmer' +version = '1.7.3' + +homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3' +description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible +with both version 2 and version 3 of the HMMER package from http://hmmer.org.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] +sources = [SOURCE_TAR_GZ] +checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246'] + +dependencies = [ + ('Perl', '5.34.1'), + ('BioPerl', '1.7.8'), +] + +options = {'modulename': 'Bio::SearchIO::hmmer3'} + +sanity_check_paths = { + 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb index 5b7057ffa262..72311a255bbe 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-11.3.0.eb @@ -36,7 +36,12 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], }), - ('BioPerl', version, { + ('Bio::DB::SeqFeature', '1.7.4', { + 'source_tmpl': 'Bio-DB-SeqFeature-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['f2304f95fb77a12732b1883817525609e54fa70b2638ed2de0696d503407fe91'], + }), + (name, version, { 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], }), diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-11.3.0.eb new file mode 100644 index 000000000000..29cad67bb976 --- /dev/null +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.24.0-GCC-11.3.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +# Updated to 0.23.1 +# J. Sassmannshausen NHS/GSTT + +easyblock = 'Tarball' + +name = 'Bismark' +version = '0.24.0' + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/bismark/' +description = "A tool to map bisulfite converted sequence reads and determine cytosine methylation states" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/FelixKrueger/Bismark/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['dd58957bd6eac44f3a6e74e9a5ef69c8d19da0e0b64feb7d019a994fe6087d7d'] + +dependencies = [ + ('Perl', '5.34.1'), + ('Bowtie2', '2.4.5'), + ('SAMtools', '1.16.1'), +] + +sanity_check_commands = ['bismark --help'] + +sanity_check_paths = { + 'files': ['bismark', 'bismark2bedGraph', 'bismark2report', 'bismark_genome_preparation', + 'bismark_methylation_extractor', 'coverage2cytosine', 'deduplicate_bismark'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..36f8bac232a7 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.40', '', SYSTEM), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.1.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..859d6c75e5a4 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.8.2-GCCcore-13.1.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.8.2' + +homepage = 'https://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['06c9e13bdf7eb24d4ceb6b59205a4f67c2c7e7213119644430fe82fbd14a0abb'] + +builddependencies = [ + ('M4', '1.4.19'), + # use same binutils version that was used when building GCCcore toolchain + ('binutils', '2.40', '', SYSTEM), +] + + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.5.0-linux-x86_64-CUDA-11.7.0.eb b/easybuild/easyconfigs/b/Blender/Blender-3.5.0-linux-x86_64-CUDA-11.7.0.eb new file mode 100644 index 000000000000..b63f52585f9b --- /dev/null +++ b/easybuild/easyconfigs/b/Blender/Blender-3.5.0-linux-x86_64-CUDA-11.7.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PackedBinary' + +name = 'Blender' +version = '3.5.0' +versionsuffix = '-linux-x86_64-CUDA-%(cudaver)s' + +homepage = 'https://www.blender.org/' +description = """Blender is the free and open source 3D creation suite. It supports + the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, + compositing and motion tracking, even video editing and game creation.""" + +toolchain = SYSTEM + +source_urls = ['https://ftp.nluug.nl/pub/graphics/blender/release/Blender%(version_major_minor)s/'] +sources = ['blender-%(version)s-linux-x64.tar.xz'] +checksums = ['a74d52822d5753a1ffb617ac764bbacc12a4a6dec4c2b91e90cc2935a40fff68'] + +dependencies = [ + ('CUDA', '11.7.0') +] + +sanity_check_paths = { + 'files': ['blender', 'blender-softwaregl'], + 'dirs': ['%(version_major_minor)s'], +} + +sanity_check_commands = ["blender --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..eb9097baf3e3 --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Blitz++' +version = '1.0.2' + +homepage = 'https://github.com/blitzpp/blitz' + +description = """ + Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation + in C++ with a speed comparable to Fortran implementations, while preserving an + object-oriented interface +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [('https://github.com/blitzpp/blitz/archive/')] +sources = ['%(version)s.tar.gz'] +patches = ['blitz-%(version)s_pkgconfig.patch'] +checksums = [ + {'1.0.2.tar.gz': '500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2'}, + {'blitz-1.0.2_pkgconfig.patch': 'd15fb397e75eb009809ecacdd7f2f154ff05e6586895f3b0511d0b53a6e3b9fe'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3') +] + +sanity_check_paths = { + 'files': ['lib64/libblitz.a', 'lib64/libblitz.%s' % SHLIB_EXT], + 'dirs': ['include/blitz/array', 'include/blitz/meta', + 'include/random', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..a3e524a900f5 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Blosc' +version = '1.21.3' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['941016c4564bca662080bb01aea74f06630bd665e598c6f6967fd91b2e2e0bb6'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', + 'lib/libblosc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..8eb833b9f41d --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Blosc2' +version = '2.8.0' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['be608cdf68deb02e0d3ee62e183942a0fe5d5d3185375b9b6566e2ae35a9bdbd'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', + 'lib/libblosc2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb b/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb new file mode 100644 index 000000000000..663a6d225c61 --- /dev/null +++ b/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'BoltzTraP2' +version = '22.12.1' + +homepage = 'https://www.boltztrap.org' +description = """BoltzTraP2 provides a numerically stable and efficient +method for obtaining analytic representations of electronic bands based +on density-functional-theory results for relatively sparse grids. It +achieves this goal by using smoothed Fourier interpolation.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('pyFFTW', '0.13.1'), + ('spglib', '2.0.2'), + ('Eigen', '3.4.0'), + ('matplotlib', '3.5.2'), + ('ASE', '3.22.1'), + ('netcdf4-python', '1.6.1'), + ('VTK', '9.2.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'BoltzTraP2', + 'patches': ['BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch'], + 'checksums': [ + {'BoltzTraP2-22.12.1.tar.gz': '8338d600c509705e40c834b5431ee8a556d87b06aa1a09853031960a1ff65b3e'}, + {'BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch': + '63791c73ffcb36c0615111377ac5666abfce48872800d3bcc8c93113e37c9030'}, + ], + }), +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch b/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch new file mode 100644 index 000000000000..ccf7129bb7b9 --- /dev/null +++ b/easybuild/easyconfigs/b/BoltzTraP2/BoltzTraP2-22.12.1_use_EB_spglib+eigen.patch @@ -0,0 +1,51 @@ +Use spglib and Eigen from EB install + +Åke Sandgren, 2023-04-17 +diff -ru BoltzTraP2-22.12.1.orig/setup.py BoltzTraP2-22.12.1/setup.py +--- BoltzTraP2-22.12.1.orig/setup.py 2022-12-19 19:38:59.000000000 +0100 ++++ BoltzTraP2-22.12.1/setup.py 2023-04-17 12:32:46.654682662 +0200 +@@ -187,7 +187,8 @@ + + def run(self): + """Run build_spglib and then delegate on the normal build_ext.""" +- self.run_command("build_spglib") ++ # Use spglib from EB installation ++ # self.run_command("build_spglib") + DefaultBuildExtCommand.run(self) + + +@@ -213,12 +214,6 @@ + else: + extension = "cpp" + +-eigen_dir = os.path.abspath( +- os.path.join( +- os.path.dirname(__file__), "external", "eigen-eigen-3215c06819b9" +- ) +-) +- + extensions = [ + Extension( + "BoltzTraP2.sphere.frontend", +@@ -228,10 +223,10 @@ + ], + language="c++", + include_dirs=INCLUDE_DIRS +- + [np.get_include(), BuildSPGlibCommand.header_dir, eigen_dir], ++ + [np.get_include()], + library_dirs=LIBRARY_DIRS, + runtime_library_dirs=LIBRARY_DIRS, +- extra_objects=[BuildSPGlibCommand.static_library], ++ libraries = ['symspg'], + ) + ] + +@@ -282,8 +277,6 @@ + ext_modules=extensions, + cmdclass={ + "build_ext": BuildExtCommand, +- "build_spglib": BuildSPGlibCommand, +- "clean_spglib": CleanSPGlibCommand, + }, + install_requires=[ + "spglib", diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.76.0-gompi-2021a.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.76.0-gompi-2021a.eb new file mode 100644 index 000000000000..9a5bff9bd315 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.76.0-gompi-2021a.eb @@ -0,0 +1,29 @@ +easyblock = 'EB_Boost' + +name = 'Boost.MPI' +version = '1.76.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['7bd7ddceec1a1dfdcbdb3e609b60d01739c38390a5f956385a12f3122049f0ca'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('zstd', '1.4.9'), + ('ICU', '69.1'), +] + +configopts = '--without-libraries=python' + +boost_mpi = True +tagged_layout = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb index f0fce1ec0afa..efefe29ecc3d 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.77.0-intel-compilers-2021.4.0.eb @@ -24,6 +24,8 @@ preconfigopts = "sed -i 's/-static//g' tools/build/src/engine/build.sh && " # see also https://github.com/boostorg/build/issues/647 preconfigopts += "sed -i 's/{TOOLSET}/{B2_TOOLSET}/g' tools/build/src/engine/build.sh && " +configopts = '--without-libraries=python,mpi' + # disable MPI, build Boost libraries with tagged layout boost_mpi = False tagged_layout = True diff --git a/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.7-foss-2022a.eb b/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.7-foss-2022a.eb new file mode 100644 index 000000000000..ddcca5a30f17 --- /dev/null +++ b/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.7-foss-2022a.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Bottleneck' +version = '1.3.7' + +homepage = 'https://kwgoodman.github.io/bottleneck-doc' +description = "Fast NumPy array functions written in C" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e1467e373ad469da340ed0ff283214d6531cc08bfdca2083361a3aa6470681f8'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb new file mode 100644 index 000000000000..10e39d0b33ef --- /dev/null +++ b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'Braindecode' +version = '0.7' +versionsuffix = '-PyTorch-1.10.0-CUDA-%(cudaver)s' + +homepage = 'https://braindecode.org/' +description = """Braindecode is an open-source Python toolbox for decoding raw +electrophysiological brain data with deep learning models. It includes dataset +fetchers, data preprocessing and visualization tools, as well as +implementations of several deep learning architectures and data augmentations +for analysis of EEG, ECoG and MEG.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('h5py', '3.2.1'), + ('matplotlib', '3.4.2'), + ('MNE-Python', '0.24.1'), + ('MOABB', '0.4.6'), + ('skorch', '0.11.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['e2bca3d096b70b041d7b30ca2dfeaffae79ea722a4578cee04c9864ec07effce'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0.eb b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0.eb new file mode 100644 index 000000000000..9780e1b0bc12 --- /dev/null +++ b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.7-foss-2021a-PyTorch-1.10.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'Braindecode' +version = '0.7' +versionsuffix = '-PyTorch-1.10.0' + +homepage = 'https://braindecode.org/' +description = """Braindecode is an open-source Python toolbox for decoding raw +electrophysiological brain data with deep learning models. It includes dataset +fetchers, data preprocessing and visualization tools, as well as +implementations of several deep learning architectures and data augmentations +for analysis of EEG, ECoG and MEG.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('h5py', '3.2.1'), + ('matplotlib', '3.4.2'), + ('MNE-Python', '0.24.1'), + ('MOABB', '0.4.6'), + ('skorch', '0.11.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['e2bca3d096b70b041d7b30ca2dfeaffae79ea722a4578cee04c9864ec07effce'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..36c52aae8f75 --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Brotli' +version = '1.0.9' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/google/brotli/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['Brotli-%(version)s_pc_link_flags.patch'] +checksums = [ + 'f9e8d81d0405ba66d181529af42a3354f838c939095ff99930da6aa9cdf6fe46', # v1.0.9.tar.gz + '1a8498fe5179fa530d5e6da57632a7ca8ee98b462953b9995e3400cdac4c3d7e', # Brotli-1.0.9_pc_link_flags.patch +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT, + 'lib/libbrotlidec-static.a', 'lib/libbrotlienc-static.a'], + 'dirs': [], +} + +sanity_check_commands = ["brotli --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..e9d6adbb76fd --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """Brunsli is a lossless JPEG repacking library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Highway', '1.0.4'), +] + +# skip use of third_party directory, since we provide Brotli via a proper dependency +preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' + +buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" + +# also install dbrunsli binary and missing libraries +postinstallcmds = [ + "mkdir %(installdir)s/bin", + "cp dbrunsli %(installdir)s/bin/", + "cp libbrunsli*.a %(installdir)s/lib*/", + "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, +] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['include/brunsli', 'lib'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb index db9e0c95129d..f882fbbd8381 100644 --- a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.0-GCCcore-10.3.0.eb @@ -1,4 +1,4 @@ -easyblock = 'Binary' +easyblock = 'Cargo' name = 'bamtofastq' version = '1.4.0' @@ -8,9 +8,345 @@ description = """Convert 10x BAM files to the original FASTQs compatible with 10 toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +crates = [ + ('anyhow', '1.0.44'), + ('backtrace', '0.3.61'), + ('addr2line', '0.16.0'), + ('gimli', '0.25.0'), + ('cfg-if', '1.0.0'), + ('libc', '0.2.103'), + ('miniz_oxide', '0.4.4'), + ('adler', '1.0.2'), + ('autocfg', '1.0.1'), + ('object', '0.26.2'), + ('memchr', '2.4.1'), + ('rustc-demangle', '0.1.21'), + ('cc', '1.0.71'), + ('jobserver', '0.1.24'), + ('libc', '0.2.103'), + ('backtrace', '0.3.61'), + ('bincode', '1.3.3'), + ('serde', '1.0.130'), + ('serde_derive', '1.0.130'), + ('proc-macro2', '1.0.29'), + ('unicode-xid', '0.2.2'), + ('quote', '1.0.10'), + ('proc-macro2', '1.0.29'), + ('syn', '1.0.80'), + ('proc-macro2', '1.0.29'), + ('quote', '1.0.10'), + ('unicode-xid', '0.2.2'), + ('csv', '1.1.6'), + ('bstr', '0.2.17'), + ('lazy_static', '1.4.0'), + ('memchr', '2.4.1'), + ('regex-automata', '0.1.10'), + ('serde', '1.0.130'), + ('csv-core', '0.1.10'), + ('memchr', '2.4.1'), + ('itoa', '0.4.8'), + ('ryu', '1.0.5'), + ('serde', '1.0.130'), + ('docopt', '1.1.1'), + ('lazy_static', '1.4.0'), + ('regex', '1.5.4'), + ('aho-corasick', '0.7.18'), + ('memchr', '2.4.1'), + ('memchr', '2.4.1'), + ('regex-syntax', '0.6.25'), + ('serde', '1.0.130'), + ('strsim', '0.10.0'), + ('flate2', '1.0.22'), + ('cfg-if', '1.0.0'), + ('crc32fast', '1.2.1'), + ('cfg-if', '1.0.0'), + ('libc', '0.2.103'), + ('libz-sys', '1.1.3'), + ('libc', '0.2.103'), + ('cc', '1.0.71'), + ('cmake', '0.1.45'), + ('cc', '1.0.71'), + ('pkg-config', '0.3.20'), + ('itertools', '0.10.1'), + ('either', '1.6.1'), + ('regex', '1.5.4'), + ('rust-htslib', '0.38.2'), + ('bio-types', '0.12.0'), + ('derive-new', '0.5.9'), + ('proc-macro2', '1.0.29'), + ('quote', '1.0.10'), + ('syn', '1.0.80'), + ('lazy_static', '1.4.0'), + ('regex', '1.5.4'), + ('strum_macros', '0.20.1'), + ('heck', '0.3.3'), + ('unicode-segmentation', '1.8.0'), + ('proc-macro2', '1.0.29'), + ('quote', '1.0.10'), + ('syn', '1.0.80'), + ('thiserror', '1.0.29'), + ('thiserror-impl', '1.0.29'), + ('proc-macro2', '1.0.29'), + ('quote', '1.0.10'), + ('syn', '1.0.80'), + ('byteorder', '1.4.3'), + ('custom_derive', '0.1.7'), + ('derive-new', '0.5.9'), + ('hts-sys', '2.0.2'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('libc', '0.2.103'), + ('cc', '1.0.71'), + ('pkg-config', '0.3.20'), + ('libdeflate-sys', '0.5.0'), + ('cc', '1.0.71'), + ('libz-sys', '1.1.3'), + ('lzma-sys', '0.1.17'), + ('libc', '0.2.103'), + ('cc', '1.0.71'), + ('pkg-config', '0.3.20'), + ('cc', '1.0.71'), + ('fs-utils', '1.1.4'), + ('quick-error', '1.2.3'), + ('glob', '0.3.0'), + ('ieee754', '0.2.6'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.103'), + ('linear-map', '1.2.0'), + ('newtype_derive', '0.1.6'), + ('rustc_version', '0.1.7'), + ('semver', '0.1.20'), + ('regex', '1.5.4'), + ('thiserror', '1.0.29'), + ('url', '2.2.2'), + ('form_urlencoded', '1.0.1'), + ('matches', '0.1.9'), + ('percent-encoding', '2.1.0'), + ('idna', '0.2.3'), + ('matches', '0.1.9'), + ('unicode-bidi', '0.3.7'), + ('unicode-normalization', '0.1.19'), + ('tinyvec', '1.5.0'), + ('tinyvec_macros', '0.1.0'), + ('matches', '0.1.9'), + ('percent-encoding', '2.1.0'), + ('serde', '1.0.130'), + ('serde_bytes', '0.11.5'), + ('serde', '1.0.130'), + ('serde_derive', '1.0.130'), + ('shardio', '0.8.1'), + ('anyhow', '1.0.44'), + ('bincode', '1.3.3'), + ('byteorder', '1.4.3'), + ('crossbeam-channel', '0.5.1'), + ('cfg-if', '1.0.0'), + ('crossbeam-utils', '0.8.5'), + ('cfg-if', '1.0.0'), + ('lazy_static', '1.4.0'), + ('log', '0.4.14'), + ('cfg-if', '1.0.0'), + ('lz4', '1.23.2'), + ('libc', '0.2.103'), + ('lz4-sys', '1.9.2'), + ('libc', '0.2.103'), + ('cc', '1.0.71'), + ('min-max-heap', '1.3.0'), + ('serde', '1.0.130'), + ('tempfile', '3.2.0'), + ('cfg-if', '1.0.0'), + ('libc', '0.2.103'), + ('rand', '0.8.4'), + ('libc', '0.2.103'), + ('rand_chacha', '0.3.1'), + ('ppv-lite86', '0.2.10'), + ('rand_core', '0.6.3'), + ('getrandom', '0.2.3'), + ('cfg-if', '1.0.0'), + ('libc', '0.2.103'), + ('rand_core', '0.6.3'), + ('remove_dir_all', '0.5.3'), + ('redox_syscall', '0.2.10'), + ('winapi', '0.3.9'), + ('vcpkg', '0.2.15'), + ('curl-sys', '0.4.49+curl-7.79.1'), + ('openssl-sys', '0.9.67'), + ('rand_hc', '0.3.1'), + ('bitflags', '1.3.2'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('openssl-src', '111.16.0+1.1.1l'), + ('wasi', '0.10.2+wasi-snapshot-preview1'), +] source_urls = ['https://github.com/10XGenomics/bamtofastq/archive/refs/tags'] -sources = ['v%(version)s.tar.gz'] -checksums = ['b51d32e8aee3b9ace08c54397fddb590209571f47f4051077bcb22b98ca3a5ed'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = [ + {'bamtofastq-1.4.0.tar.gz': 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['bin/%(namelower)s'], 'dirs': [], diff --git a/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2021a.eb b/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2021a.eb new file mode 100644 index 000000000000..8fc66740160e --- /dev/null +++ b/easybuild/easyconfigs/b/batchgenerators/batchgenerators-0.25-foss-2021a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'batchgenerators' +version = '0.25' + +homepage = 'https://github.com/MIC-DKFZ/batchgenerators' +description = """Data augmentation toolkit developed at the Division of Medical +Image Computing at the German Cancer Research Center (DKFZ) to suit all our +deep learning data augmentation needs.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['38a67413e847ff367e64abac36331fcb065494202d526ae96f7644de3a0e5495'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('scikit-image', '0.18.3'), + ('scikit-learn', '0.24.2'), +] + +# remove requirement on Pillow and unittest2, which are not actually used +preinstallopts = "sed -i '13d;19d' setup.py &&" + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb new file mode 100644 index 000000000000..66fc839020be --- /dev/null +++ b/easybuild/easyconfigs/b/bcbio-gff/bcbio-gff-0.7.0-foss-2020b.eb @@ -0,0 +1,42 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to v0.6.7 +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'bcbio-gff' +version = '0.7.0' + +homepage = 'https://github.com/chapmanb/bcbb/tree/master/gff' + +description = """ +Read and write Generic Feature Format (GFF) with Biopython integration. +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['f7b3922ee274106f8716703f41f05a1795aa9d73e903f4e481995ed8f5f65d2d'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Biopython', '1.78'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +local_bcbiogffroot = 'lib/python%(pyshortver)s/site-packages' +local_targets = ['GFFOutput.py', 'GFFParser.py'] + +sanity_check_paths = { + 'files': [local_bcbiogffroot + '/BCBio/GFF/%s' % x for x in local_targets], + 'dirs': [local_bcbiogffroot], +} + +options = {'modulename': 'BCBio.GFF'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..db717c869d8c --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.40' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['d7f82c4047decf43a6f769ac32456a92ddb6932409a585c633cdd4e9df23d956'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', SYSTEM) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.2.13'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.1.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..10be685a8058 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.40-GCCcore-13.1.0.eb @@ -0,0 +1,31 @@ +name = 'binutils' +version = '2.40' + +homepage = 'https://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['d7f82c4047decf43a6f769ac32456a92ddb6932409a585c633cdd4e9df23d956'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', SYSTEM) +] + +dependencies = [ + # zlib is a runtime dep to avoid that it gets embedded in libbfd.so, + # see https://github.com/easybuilders/easybuild-easyblocks/issues/1350 + ('zlib', '1.2.13'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.40.eb b/easybuild/easyconfigs/b/binutils/binutils-2.40.eb new file mode 100644 index 000000000000..a04b02ae921f --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.40.eb @@ -0,0 +1,26 @@ +name = 'binutils' +version = '2.40' + +homepage = 'https://directory.fsf.org/project/binutils/' + +description = "binutils: GNU binary utilities" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['d7f82c4047decf43a6f769ac32456a92ddb6932409a585c633cdd4e9df23d956'] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.13'), +] + +# avoid build failure when makeinfo command is not available +# see https://sourceware.org/bugzilla/show_bug.cgi?id=15345 +buildopts = 'MAKEINFO=true' +installopts = buildopts + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb b/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb new file mode 100644 index 000000000000..62dfa0f74a11 --- /dev/null +++ b/easybuild/easyconfigs/b/biobambam2/biobambam2-2.0.87-GCC-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'biobambam2' +version = '2.0.87' + +homepage = 'https://github.com/gt1/biobambam2' +description = "Tools for processing BAM files" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/gt1/biobambam2/archive/'] +sources = ['%(version)s-release-20180301132713.tar.gz'] +checksums = ['a90500e547465d8d0455bda7936e0b660c0fd3f1b243083ec0739527f802dcf4'] + +dependencies = [ + ('libmaus2', '2.0.499'), +] + +configopts = "--with-libmaus2=$EBROOTLIBMAUS2" + +local_binaries = ['bamcollate2', 'bammarkduplicates', 'bammaskflags', 'bamrecompress', + 'bamsormadup', 'bamsort', 'bamtofastq'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["%s --help" % x for x in local_binaries] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/biom-format/biom-format-2.1.14-foss-2022a.eb b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.14-foss-2022a.eb new file mode 100644 index 000000000000..e518ffc27935 --- /dev/null +++ b/easybuild/easyconfigs/b/biom-format/biom-format-2.1.14-foss-2022a.eb @@ -0,0 +1,47 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Revised BSD +# +# Notes:: updated by Kenneth Hoste (HPC-UGent) for foss/2021b +## + +easyblock = 'PythonPackage' + +name = 'biom-format' +version = '2.1.14' + +homepage = 'https://biom-format.org' +description = """ +The BIOM file format (canonically pronounced biome) is designed to be + a general-use format for representing biological sample by observation + contingency tables. BIOM is a recognized standard for the Earth Microbiome + Project and is a Genomics Standards Consortium supported project. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c8bac94ab6aa8226c0d38af7a3341d65e5f3664b9f45ec44fdf8b5275b2f92c1'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/biom'], + 'dirs': ['lib'], +} + +options = {'modulename': 'biom'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/breseq/breseq-0.38.1-foss-2022a.eb b/easybuild/easyconfigs/b/breseq/breseq-0.38.1-foss-2022a.eb new file mode 100644 index 000000000000..7d1f5285c686 --- /dev/null +++ b/easybuild/easyconfigs/b/breseq/breseq-0.38.1-foss-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'breseq' +version = '0.38.1' + +homepage = 'https://barricklab.org/breseq' +description = "breseq is a computational pipeline for the analysis of short-read re-sequencing data" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/barricklab/breseq/releases/download/v%(version)s/'] +sources = ['breseq-%(version)s-Source.tar.gz'] +checksums = ['92af34f7248f7c8cf65951e1b86ffc0d6f7446dbe9d3323aa43c577ea1ff48b3'] + +dependencies = [ + ('R', '4.2.1'), + ('Bowtie2', '2.4.5'), + ('zlib', '1.2.12'), + ('ncurses', '6.3'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/breseq', 'bin/gdtools'], + 'dirs': [], +} + +# breseq --help exists with non-zero exit code, so use grep +sanity_check_commands = ["breseq --help | grep 'Usage: breseq'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb b/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb new file mode 100644 index 000000000000..4c80ab3d18fc --- /dev/null +++ b/easybuild/easyconfigs/b/build/build-0.10.0-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'build' +version = '0.10.0' + +homepage = 'https://github.com/pypa/build' +description = """A simple, correct Python build frontend.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyproject_hooks', '1.0.0', { + 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], + }), + (name, version, { + 'checksums': ['d5b71264afdb5951d6704482aac78de887c80691c52b88a9ad195983ca2c9269'], + }), +] + +sanity_check_commands = [ + "python3 -m build -V", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b-CUDA-12.0.0.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b-CUDA-12.0.0.eb new file mode 100644 index 000000000000..c3821707135e --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b-CUDA-12.0.0.eb @@ -0,0 +1,20 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('CUDA', '12.0.0', '', SYSTEM), + ('UCX-CUDA', '1.13.1', versionsuffix), + ('UCC-CUDA', '1.1.0', versionsuffix), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b.eb new file mode 100644 index 000000000000..1638fdb195d1 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2022b.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2022b'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2022b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2022b.eb new file mode 100644 index 000000000000..47b7eb84b222 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2022b.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'intel', 'version': '2022b'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.6-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.6-GCC-11.3.0.eb new file mode 100644 index 000000000000..238b5bbcf7b0 --- /dev/null +++ b/easybuild/easyconfigs/b/bwa-meth/bwa-meth-0.2.6-GCC-11.3.0.eb @@ -0,0 +1,50 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'bwa-meth' +version = '0.2.6' + +homepage = 'https://github.com/brentp/bwa-meth' +description = """Fast and accurante alignment of BS-Seq reads.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), + ('SAMtools', '1.13'), + ('BWA', '0.7.17'), +] + +use_pip = True + +exts_list = [ + ('toolshed', '0.4.6', { + 'checksums': ['23a31c177bf84244b30a9f12c7a8a17a66a2d63043ead0460c31b9ff42f9fb93'], + }), + (name, version, { + 'source_urls': ['https://github.com/brentp/bwa-meth/archive'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['c1d98aa6d34f103752de7ff3148c9586e5571417accb4a39f5bac8546dab497d'], + # fix TypeError when using --help, see https://github.com/brentp/bwa-meth/pull/87 + 'preinstallopts': "sed -i 's/44% /44%% /g' bwameth.py && ", + 'modulename': 'bwameth', + }), +] + +fix_python_shebang_for = ['bin/bwameth.py', 'bin/toolshed'] + +sanity_check_paths = { + 'files': ['bin/bwameth.py', 'bin/toolshed'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "toolshed --help", + "bwameth.py --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..cb5b2748e2be --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.40'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.1.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..e719f5aa4331 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-13.1.0.eb @@ -0,0 +1,27 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.40'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CASPR/CASPR-20200730-foss-2022a.eb b/easybuild/easyconfigs/c/CASPR/CASPR-20200730-foss-2022a.eb new file mode 100644 index 000000000000..c32f29ed00e7 --- /dev/null +++ b/easybuild/easyconfigs/c/CASPR/CASPR-20200730-foss-2022a.eb @@ -0,0 +1,39 @@ +# Author: Denis Kristak (Inuits) + +easyblock = 'Tarball' + +name = 'CASPR' +version = '20200730' +local_commit = 'b74fde2' + +homepage = 'https://judithbergada.github.io/CASPR' +description = """Running CASPR is extremely easy and convenient to analyze CRIPR-Cas9 screens using pgRNAs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/judithbergada/CASPR/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['96cd3a8fd8f1d8cddf798f07bff46c1048ab9343aa40c31d3430f1e58703f0ac'] + +dependencies = [ + ('FastQC', '0.11.9', '-Java-11', SYSTEM), + ('cutadapt', '4.2'), + ('FASTX-Toolkit', '0.0.14'), + ('STAR', '2.7.10b'), + ('SAMtools', '1.16.1'), + ('vispr', '0.4.14'), + ('R', '4.2.1'), +] + +modextrapaths = { + 'PATH': 'source/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['source'], +} + +sanity_check_commands = ["CASPR --help 2>&1 | grep 'Usage: CASPR'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb new file mode 100644 index 000000000000..8e3491edd65a --- /dev/null +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-22.11-foss-2022a.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'CASTEP' +version = '22.11' + +homepage = 'http://www.castep.org' +description = """ +CASTEP is an electronic structure materials modelling code based on density +functional theory (DFT), with functionality including geometry optimization +molecular dynamics, phonons, NMR chemical shifts and much more. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +download_instructions = """CASTEP is proprietary software, available under a free-of-charge license for academic use +only. Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license.""" + +sources = [SOURCE_TAR_GZ] +checksums = ['aca3fc2207c677561293585a4edaf233676a759c5beb8389cf938411226ef1f5'] + +# Python+numpy are needed for the elastic constants and castepconv utilities, but +# should work with any system or eb Python including 2.7. +dependencies = [ + ('Perl', '5.34.1'), +] + +skipsteps = ['configure'] + +buildopts = 'COMMS_ARCH=mpi FFT=fftw3 MATH_LIBS="-lflexiblas" FFTLIBDIR=$FFT_LIB_DIR MATHLIBDIR=$BLAS_LIB_DIR' +buildopts += ' castep tools utilities' + +preinstallopts = 'mkdir -p %(installdir)s/bin &&' +installopts = 'COMMS_ARCH=mpi FFT=fftw3 MATH_LIBS="-lflexiblas" INSTALL_DIR="%(installdir)s/bin"' +installopts += ' install-castep install-tools install-utilities' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', + 'elastics.py', 'ceteprouts.pm']], + 'dirs': [], +} + +sanity_check_commands = [ + 'castep.mpi --help', + 'optados.mpi --help', +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-11.3.0.eb new file mode 100644 index 000000000000..d2dca1af47d2 --- /dev/null +++ b/easybuild/easyconfigs/c/CDBtools/CDBtools-0.99-GCC-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'CDBtools' +version = '0.99' + +homepage = 'http://compbio.dfci.harvard.edu/tgi' +description = "CDB (Constant DataBase) indexing and retrieval tools for FASTA files" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta'] +sources = [{'download_filename': 'cdbfasta.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['68767e8b2fb9de5a6d68ee16df73293f65e02f05cf2f747a9dd6b8854766722c'] + +buildopts = 'CC="$CXX" DBGFLAGS="$CXXFLAGS"' + +files_to_copy = [(['cdbfasta', 'cdbyank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/cdbfasta', 'bin/cdbyank'], + 'dirs': [], +} + +sanity_check_commands = [ + "cdbfasta -v", + "cdbyank -v", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.4-GCC-12.2.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.4-GCC-12.2.0.eb new file mode 100644 index 000000000000..1a08a4ed224c --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.4.6.4-GCC-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.4.6.4' + +homepage = 'https://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://proj-clhep.web.cern.ch/proj-clhep/dist1/'] +sources = [SOURCELOWER_TGZ] +checksums = ['49c89330f1903ef707d3c5d79c16a7c5a6f2c90fc290e2034ee3834809489e57'] + +builddependencies = [('CMake', '3.24.3')] + +sanity_check_paths = { + 'files': ['bin/clhep-config', 'lib/libCLHEP.a', 'lib/libCLHEP.%s' % SHLIB_EXT], + 'dirs': ['include/CLHEP'], +} + +sanity_check_commands = ["clhep-config --help"] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..e7b38dfeff16 --- /dev/null +++ b/easybuild/easyconfigs/c/CLIP/CLIP-20230220-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'CLIP' +version = '20230220' +versionsuffix = '-CUDA-%(cudaver)s' +_commit = 'a9b1bf5' + +homepage = 'https://github.com/openai/CLIP' +description = """ +CLIP (Contrastive Language-Image Pre-Training) is a neural network trained on a +variety of (image, text) pairs. It can be instructed in natural language to +predict the most relevant text snippet, given an image, without directly +optimizing for the task, similarly to the zero-shot capabilities of GPT-2 and +3.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('PyTorch', '1.12.0', versionsuffix), + ('tqdm', '4.64.0'), + ('torchvision', '0.13.1', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('ftfy', '6.1.1', { + 'checksums': ['bfc2019f84fcd851419152320a6375604a0f1459c281b5b199b2cd0d2e727f8f'], + }), + (name, version, { + 'source_urls': ['https://github.com/openai/CLIP/archive'], + 'sources': [{'download_filename': _commit + '.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['9cbe833d1a8c1d5ea6db87c290119fda4d35a3fe2f7a94d6a88779de502a98e3'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb new file mode 100644 index 000000000000..b16ab7d9572e --- /dev/null +++ b/easybuild/easyconfigs/c/CMSeq/CMSeq-1.0.4-foss-2022a.eb @@ -0,0 +1,37 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'PythonPackage' + +name = 'CMSeq' +version = '1.0.4' + +homepage = 'https://github.com/SegataLab/cmseq/' +description = "CMSeq is a set of commands to provide an interface to .bam files for coverage and sequence consensus." + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['93038a6dba826e29a66df3ec8ab2b3e3872acac7af9df245e4a5a624584aca5c'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Biopython', '1.79'), + ('bcbio-gff', '0.7.0'), + ('biom-format', '2.1.14'), + ('Pysam', '0.19.1'), + ('SAMtools', '1.16.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['breadth_depth.py', 'consensus.py', 'poly.py', 'polymut.py']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..d9b8ac7afaae --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.26.3' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bbd8d39217509d163cb544a40d6428ac666ddc83e22905d3e52c925781f0f659'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('cURL', '8.0.1'), + ('libarchive', '3.6.2'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-13.1.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..ce03c3694cdb --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.26.3-GCCcore-13.1.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.26.3' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bbd8d39217509d163cb544a40d6428ac666ddc83e22905d3e52c925781f0f659'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('cURL', '8.0.1'), + ('libarchive', '3.6.2'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb new file mode 100644 index 000000000000..a979cbf28d2a --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2022.1-foss-2022a.eb @@ -0,0 +1,40 @@ +## +# Author: Robert Mijakovic +## +name = 'CP2K' +version = '2022.1' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['2c34f1a7972973c62d471cd35856f444f11ab22f2ff930f6ead20f3454fd228b'] + +# https://github.com/cp2k/cp2k/releases/download/v2022.1/cp2k-2022.1.tar.bz2 +dependencies = [ + ('Libint', '2.7.2', '-lmax-6-cp2k'), + ('libxc', '5.2.3'), + ('libxsmm', '1.17'), + ('FFTW', '3.3.10'), + ('PLUMED', '2.8.1'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), +] + +type = 'psmp' + +# regression test reports handful of failures, +# we're assuming those are OK to ignore... +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb new file mode 100644 index 000000000000..67b7353f3471 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-9.1-foss-2022a.eb @@ -0,0 +1,39 @@ +## +# Author: Robert Mijakovic +## +name = 'CP2K' +version = '9.1' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['fedb4c684a98ad857cd49b69a3ae51a73f85a9c36e9cb63e3b02320c74454ce6'] + +dependencies = [ + ('Libint', '2.7.2', '-lmax-6-cp2k'), + ('libxc', '5.2.3'), + ('libxsmm', '1.17'), + ('FFTW', '3.3.10'), + ('PLUMED', '2.8.1'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.8.2'), +] + +type = 'psmp' + +# regression test reports handful of failures, +# we're assuming those are OK to ignore... +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb new file mode 100644 index 000000000000..008b9e1c179b --- /dev/null +++ b/easybuild/easyconfigs/c/CPC2/CPC2-1.0.1-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PackedBinary' + +name = 'CPC2' +version = '1.0.1' + +homepage = 'http://cpc2.gao-lab.org/' +description = """ a fast and accurate coding potential calculator based on sequence intrinsic features """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/gao-lab/CPC2_standalone/archive/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['31f3d1e2466aea25f03ffcb5abd4556cd17862ef65ed3a1e42f3d99665529d08'] + +local_svm_orig = "lib_dir + \"libsvm/libsvm-3.18/" + +postinstallcmds = [ + "sed -i 's|" + local_svm_orig + "svm-scale\"|\"$EBROOTLIBSVM/bin/svm-scale\"|g' %(installdir)s/bin/CPC2.py", + "sed -i 's|" + local_svm_orig + "svm-predict\"|\"$EBROOTLIBSVM/bin/svm-predict\"|g' %(installdir)s/bin/CPC2.py", +] + +dependencies = [ + ('Python', '3.10.4'), + ('LIBSVM', '3.30'), + ('Biopython', '1.79'), +] + +install_cmd = 'cp -a CPC2*/{bin,data} %(installdir)s/' + +sanity_check_paths = { + 'files': ['bin/CPC2.py'], + 'dirs': [], +} + +sanity_check_commands = ['CPC2.py -i %(installdir)s/data/example.fa -o example.out'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CPLEX/CPLEX-22.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/CPLEX/CPLEX-22.1.1-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..d788295e132c --- /dev/null +++ b/easybuild/easyconfigs/c/CPLEX/CPLEX-22.1.1-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +name = 'CPLEX' +version = '22.1.1' + +homepage = 'https://www.ibm.com/analytics/cplex-optimizer' +description = """IBM ILOG CPLEX Optimizer's mathematical programming technology enables + analytical decision support for improving efficiency, + reducing costs, and increasing profitability.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = ['cplex_studio%s.linux_x86_64.bin' % ''.join(version.split('.'))] +checksums = ['ab6d3f0953fdb3cbd43854452357955ef96db8b751c0866de3572fc47a0df542'] + +download_instructions = """ +1. Visit https://www.ibm.com/products/ilog-cplex-optimization-studio +2. Sign up and download the Academic Edition +""" + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('Python', '3.9.6'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/CREST/CREST-2.11.2-intel-2021a.eb b/easybuild/easyconfigs/c/CREST/CREST-2.11.2-intel-2021a.eb new file mode 100644 index 000000000000..4746716d31da --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-2.11.2-intel-2021a.eb @@ -0,0 +1,32 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'CMakeMake' + +name = 'CREST' +version = '2.11.2' + +homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' +description = """CREST is an utility/driver program for the xtb program. Originally it was designed + as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, + but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally + the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb + program) and tool for the creation and analysation of structure ensembles. +""" + +toolchain = {'name': 'intel', 'version': '2021a'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f17da872064eb64502ac24c19e431467940d98dcb1bd391f7267f412a0a79dab'] + +builddependencies = [('CMake', '3.20.1')] + +sanity_check_paths = { + 'files': ['bin/%s' % name.lower()], + 'dirs': [], +} + +sanity_check_commands = ["crest -h", "crest --cite"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.5.2.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.5.2.eb new file mode 100644 index 000000000000..bc5895712e02 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.5.2.eb @@ -0,0 +1,26 @@ +name = 'CUDA' +version = '11.5.2' +local_nv_version = '495.29.05' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [ + { + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '74959abf02bcba526f0a3aae322c7641b25da040ccd6236d07038f81997b73a6', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + '45c468f430436b3e95d5e485a6ba0ec1fa2b23dc6c551c1307b79996ecf0a7ed', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '31337c8bdc224fa1bd07bc4b6a745798392428118cc8ea0fa4446ee4ad47dd30', + } +] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb new file mode 100644 index 000000000000..2b8fbc5a70ca --- /dev/null +++ b/easybuild/easyconfigs/c/Cantera/Cantera-2.6.0-foss-2022a.eb @@ -0,0 +1,49 @@ +easyblock = 'SCons' + +name = 'Cantera' +version = '2.6.0' + +homepage = 'https://github.com/Cantera/cantera' +description = """Chemical kinetics, thermodynamics, and transport tool suite""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/Cantera/cantera/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7273622ea76a53373cee820f939613b15eea3dd83db6e1b127c5ed043f77dc5b'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost', '1.79.0'), + ('SUNDIALS', '6.3.0'), + ('yaml-cpp', '0.7.0'), + ('ruamel.yaml', '0.17.21'), +] +builddependencies = [ + ('SCons', '4.4.0'), + ('Eigen', '3.4.0'), + ('fmt', '9.1.0'), + ('googletest', '1.11.0'), +] + +local_common_opts = 'env_vars=all CC="$CC" CXX="$CXX" cc_flags="$CFLAGS" cxx_flags="$CXXFLAGS" ' +local_common_opts += 'blas_lapack_libs=flexiblas blas_lapack_dir=$BLAS_LAPACK_LIB_DIR ' +local_common_opts += 'sundials_include=$EBROOTSUNDIALS/include sundials_libdir=$EBROOTSUNDIALS/lib' +buildopts = 'build ' + local_common_opts +# tests hang, so disable them for now +# runtest = 'test ' + local_common_opts +installopts = 'install ' + local_common_opts +prefix_arg = 'prefix=' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ck2cti'], + 'dirs': ['include/cantera', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [('python', "-c 'import cantera'")] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.3-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..ee6242554c7f --- /dev/null +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-0.10.3-GCCcore-12.2.0.eb @@ -0,0 +1,35 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to 0.9.1 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'CapnProto' +version = '0.10.3' + +homepage = 'https://capnproto.org' +description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +# -std=c++17 to avoid problems like "error: 'aligned_alloc' was not declared in this scope" +# lowopt (-O1) to avoid problems like "capnp/schema-loader.c++:1971: failed: no schema node loaded for ..." +# (only on Intel Skylake?) +toolchainopts = {'cstd': 'c++17', 'lowopt': True} + +source_urls = ['https://capnproto.org/'] +sources = ['capnproto-c++-%(version)s.tar.gz'] +checksums = ['97fde3cf05129db919453af4ef6c6a415662111c2e6e9b5194e2566d44b8507a'] + +builddependencies = [('binutils', '2.39')] + +local_bins = ['capnp', 'capnpc', 'capnpc-c++', 'capnpc-capnp'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['include/capnp', 'include/kj', 'lib'], +} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..13264c0021f2 --- /dev/null +++ b/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'Casanovo' +version = '3.3.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://casanovo.readthedocs.io' +description = "De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model" + +toolchain = {'name': 'foss', 'version': '2022a'} + +use_pip = True + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('h5py', '3.7.0'), + ('lxml', '4.9.1'), + ('einops', '0.4.1'), + ('PyTorch', '1.12.0', versionsuffix), + ('PyTorch-Lightning', '1.8.4', versionsuffix), + ('scikit-learn', '1.1.2'), + ('numba', '0.56.4', versionsuffix), + ('tensorboard', '2.10.0'), +] + +exts_list = [ + ('pyteomics', '4.5.6', { + 'checksums': ['8c6e79068f18d853218967a312c22861422df69fdcf62499a258526f687b126f'], + }), + ('depthcharge-ms', '0.1.0', { + 'checksums': ['237f8e70fd237fdc945882e981170321ac7da2638ba24b52f72dad9ff2262096'], + 'modulename': 'depthcharge', + }), + ('natsort', '8.3.1', { + 'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'], + }), + ('PyGithub', '1.58.1', { + 'checksums': ['7d528b4ad92bc13122129fafd444ce3d04c47d2d801f6446b6e6ee2d410235b3'], + 'modulename': 'github', + }), + ('Deprecated', '1.2.13', { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), + ('fastobo', '0.12.2', { + 'checksums': ['2f2779f70ac54874329dddc74cabd86fea88abe56c544c2238076c1d27fe045e'], + }), + ('lark', '1.1.5', { + 'checksums': ['4b534eae1f9af5b4ea000bea95776350befe1981658eea3820a01c37e504bb4d'], + }), + ('spectrum-utils', '0.4.1', { + 'sources': ['spectrum_utils-%(version)s.tar.gz'], + 'checksums': ['c4f1c80de8144fb8d6fc276968ef4d5e896dad03bb8a9316f69c73ee82affd85'], + }), + ('casanovo', version, { + 'checksums': ['d9358c64a549d00f0568ebef65d5500ad63041e9ea2ebd348a7e650c8177ff81'], + }), +] + +sanity_check_paths = { + 'files': ['bin/casanovo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["casanovo --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a.eb b/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a.eb new file mode 100644 index 000000000000..8318aafc346c --- /dev/null +++ b/easybuild/easyconfigs/c/Casanovo/Casanovo-3.3.0-foss-2022a.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'Casanovo' +version = '3.3.0' + +homepage = 'https://casanovo.readthedocs.io' +description = "De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model" + +toolchain = {'name': 'foss', 'version': '2022a'} + +use_pip = True + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('h5py', '3.7.0'), + ('lxml', '4.9.1'), + ('einops', '0.4.1'), + ('PyTorch', '1.12.0'), + ('PyTorch-Lightning', '1.8.4'), + ('scikit-learn', '1.1.2'), + ('numba', '0.56.4'), + ('tensorboard', '2.10.0'), +] + +exts_list = [ + ('pyteomics', '4.5.6', { + 'checksums': ['8c6e79068f18d853218967a312c22861422df69fdcf62499a258526f687b126f'], + }), + ('depthcharge-ms', '0.1.0', { + 'checksums': ['237f8e70fd237fdc945882e981170321ac7da2638ba24b52f72dad9ff2262096'], + 'modulename': 'depthcharge', + }), + ('natsort', '8.3.1', { + 'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'], + }), + ('PyGithub', '1.58.1', { + 'checksums': ['7d528b4ad92bc13122129fafd444ce3d04c47d2d801f6446b6e6ee2d410235b3'], + 'modulename': 'github', + }), + ('Deprecated', '1.2.13', { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), + ('fastobo', '0.12.2', { + 'checksums': ['2f2779f70ac54874329dddc74cabd86fea88abe56c544c2238076c1d27fe045e'], + }), + ('lark', '1.1.5', { + 'checksums': ['4b534eae1f9af5b4ea000bea95776350befe1981658eea3820a01c37e504bb4d'], + }), + ('spectrum-utils', '0.4.1', { + 'sources': ['spectrum_utils-%(version)s.tar.gz'], + 'checksums': ['c4f1c80de8144fb8d6fc276968ef4d5e896dad03bb8a9316f69c73ee82affd85'], + }), + ('casanovo', version, { + 'checksums': ['d9358c64a549d00f0568ebef65d5500ad63041e9ea2ebd348a7e650c8177ff81'], + }), +] + +sanity_check_paths = { + 'files': ['bin/casanovo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["casanovo --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a.eb new file mode 100644 index 000000000000..8b0c66ef249b --- /dev/null +++ b/easybuild/easyconfigs/c/CellChat/CellChat-1.5.0-foss-2022a.eb @@ -0,0 +1,56 @@ +easyblock = 'Bundle' + +name = 'CellChat' +version = '1.5.0' + +homepage = 'https://github.com/sqjin/CellChat' +description = """" +R toolkit for inference, visualization and analysis of cell-cell communication +from single-cell data""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', '-R-%(rver)s'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('umap-learn', '0.5.3'), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} + +exts_list = [ + ('ggalluvial', '0.12.5', { + 'checksums': ['90044c880e70096137a733d601b11e558fe55e4e7d3aaacac6f08d7847415d71'], + }), + ('systemfonts', '1.0.4', { + 'checksums': ['ef766c75b942f147d382664a00d6a4930f1bfe0cce9d88943f571682a85a84c0'], + }), + ('svglite', '2.1.1', { + 'checksums': ['48700169eec1b05dbee9e2bae000aa84c544617b018cb3ac431a128cfd8dac56'], + }), + (name, version, { + 'preinstallopts': "rm src/*.o src/*.so && ", + 'source_urls': ['https://github.com/sqjin/CellChat/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['c9e31327cbbcf1fec5e6d8a0dfe011ded8e543557107e93dd4a417c4c137d1c6'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellOracle/CellOracle-0.12.0-foss-2022a.eb b/easybuild/easyconfigs/c/CellOracle/CellOracle-0.12.0-foss-2022a.eb new file mode 100644 index 000000000000..e712870108d9 --- /dev/null +++ b/easybuild/easyconfigs/c/CellOracle/CellOracle-0.12.0-foss-2022a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'CellOracle' +version = '0.12.0' + +homepage = 'https://github.com/morris-lab/CellOracle' +description = """CellOracle is a Python library for in silico gene perturbation analyses using single-cell omics data +and Gene Regulatory Network models.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('R', '4.2.1'), + ('SciPy-bundle', '2022.05'), + ('numba', '0.56.4'), + ('matplotlib', '3.5.2'), + ('Seaborn', '0.12.1'), + ('scikit-learn', '1.1.2'), + ('h5py', '3.7.0'), + ('velocyto', '0.17.17'), + ('umap-learn', '0.5.3'), + ('Arrow', '8.0.0'), + ('tqdm', '4.64.0'), + ('igraph', '0.10.3'), + ('IPython', '8.5.0'), + ('scanpy', '1.9.1'), + ('GOATOOLS', '1.3.1'), + ('genomepy', '0.15.0'), + ('GimmeMotifs', '0.17.2'), + ('Qtconsole', '5.4.0'), +] + +use_pip = True + +# remove louvain from requirements, since CellOracle doesn't actually use it at all +local_preinstallopts = "sed -i '/louvain/d' requirements.txt && " +# drop strict version requirement for gimmemotifs dependency +local_preinstallopts += "sed -i 's/gimmemotifs.*/gimmemotifs/g' requirements.txt && " + +exts_list = [ + ('jupyter-console', '6.4.4', { + 'sources': ['jupyter_console-%(version)s.tar.gz'], + 'checksums': ['172f5335e31d600df61613a97b7f0352f2c8250bbd1092ef2d658f77249f89fb'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('celloracle', version, { + 'checksums': ['9d533ee3e8c14828b6859ea195e92d184b050b0782fee430eda3b01359a564d5'], + 'preinstallopts': local_preinstallopts, + }), +] + +sanity_check_commands = ["python -c 'import celloracle; celloracle.check_python_requirements()'"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..f1ca4ac1035a --- /dev/null +++ b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'Check' +version = '0.15.2' + +homepage = 'https://libcheck.github.io/check/' +description = """ +Check is a unit testing framework for C. It features a simple interface for +defining unit tests, putting little in the way of the developer. Tests are +run in a separate address space, so both assertion failures and code errors +that cause segmentation faults or other signals can be caught. Test results +are reportable in the following: Subunit, TAP, XML, and a generic logging +format.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'libcheck' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['998d355294bb94072f40584272cf4424571c396c631620ce463f6ea97aa67d2e'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = "--disable-build-docs" + +sanity_check_paths = { + 'files': ['bin/checkmk', 'lib/libcheck.a', 'lib/libcheck.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..dea2f244ad36 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-15.0.5-GCCcore-11.3.0.eb @@ -0,0 +1,58 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '15.0.5' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-project-%(version)s.src.tar.xz', +] +checksums = ['9c4278a6b8884eb7f4ae7dfe3c8e5445019824885e47cfdf1392563c47316fd6'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Perl', '5.34.1'), + ('elfutils', '0.187'), + # Including Python bindings would require this as a runtime dep + ('Python', '3.10.4'), +] +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.38'), + ('hwloc', '2.7.1'), + ('libxml2', '2.9.13'), + ('ncurses', '6.3'), + ('GMP', '6.2.1'), + ('Z3', '4.10.2'), +] + +# enabling RTTI makes the flang compiler need to link to libc++ so instead of +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 +# you would need +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 -l c++ +enable_rtti = False + +assertions = True +python_bindings = False +skip_all_tests = True + +llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi'] +llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.2.0.eb b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.2.0.eb new file mode 100644 index 000000000000..df007a1ade50 --- /dev/null +++ b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-10.2.0.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by Adam Huffman +# Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Clustal-Omega' +version = '1.2.4' + +homepage = 'http://www.clustal.org/omega/' +description = """ Clustal Omega is a multiple sequence alignment + program for proteins. It produces biologically meaningful multiple + sequence alignments of divergent sequences. Evolutionary relationships + can be seen via viewing Cladograms or Phylograms """ + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'openmp': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8683d2286d663a46412c12a0c789e755e7fd77088fb3bc0342bb71667f05a3ee'] + +dependencies = [('argtable', '2.13')] + +sanity_check_paths = { + 'files': ['bin/clustalo'], + 'dirs': [], +} + +sanity_check_commands = ["clustalo --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb index 5d220aff8506..636bef3b8e8d 100644 --- a/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb @@ -27,7 +27,7 @@ install_cmd = "cp -r %(builddir)s/* %(installdir)s/ && " install_cmd += "tar -xf %(installdir)s/%(name)s-%(version)s/CodAn.tar.gz && " install_cmd += "mkdir %(installdir)s/bin && " install_cmd += "mv %(installdir)s/%(name)s-%(version)s/bin/* %(installdir)s/bin && " -install_cmd += "chmod u+rwx %(installdir)s/bin/* " +install_cmd += "chmod u+rwx,go+rx %(installdir)s/bin/* " sanity_check_paths = { 'files': ['bin/%(namelower)s.py'], diff --git a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2021b.eb b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2021b.eb new file mode 100644 index 000000000000..a82e6498b5f6 --- /dev/null +++ b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0-foss-2021b.eb @@ -0,0 +1,51 @@ +easyblock = 'MakeCp' + +name = 'CodingQuarry' +version = '2.0' + +homepage = 'https://sourceforge.net/p/codingquarry' +description = "Highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'openmp': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['CodingQuarry_v%(version)s.tar.gz'] +patches = ['CodingQuarry-2.0_python3.patch'] +checksums = [ + {'CodingQuarry_v2.0.tar.gz': '1198afbf7cebcf0975c5b20d92b7a2dd6d956072fcde6e86fdce6aeae4842504'}, + {'CodingQuarry-2.0_python3.patch': '8e1b117431d8b104f2114875d8f751aa91c1c3c1b0ddd5a4f85251605c2ab9df'}, +] + +dependencies = [ + ('Python', '3.9.6'), + ('Biopython', '1.79'), +] + +buildopts = 'CFLAGS="$CFLAGS"' + +files_to_copy = [ + (['CodingQuarry', 'CufflinksGTF_to_CodingQuarryGFF3.py'], 'bin'), + 'QuarryFiles', + 'TESTING', +] + +fix_python_shebang_for = [ + 'bin/CufflinksGTF_to_CodingQuarryGFF3.py', + 'QuarryFiles/scripts/*.py', +] + +sanity_check_paths = { + 'files': ['bin/CodingQuarry', 'bin/CufflinksGTF_to_CodingQuarryGFF3.py'], + 'dirs': ['QuarryFiles/scripts', 'QuarryFiles/self_train', 'QuarryFiles/species', 'TESTING'], +} + +sanity_check_commands = [ + "CodingQuarry --help | grep '^CodingQuarry v. %(version)s'", + "mkdir -p %(builddir)s && cp -a %(installdir)s/TESTING %(builddir)s/TESTING", + "cd %(builddir)s/TESTING && CufflinksGTF_to_CodingQuarryGFF3.py Sp_transcripts.gtf > test.gff3", +] + +modextravars = {'QUARRY_PATH': '%(installdir)s/QuarryFiles'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch new file mode 100644 index 000000000000..ddf50218a42a --- /dev/null +++ b/easybuild/easyconfigs/c/CodingQuarry/CodingQuarry-2.0_python3.patch @@ -0,0 +1,36 @@ +make CufflinksGTF_to_CodingQuarryGFF3.py script compatible with Python 3.x +author: Kenneth Hoste (HPC-UGent) +--- CufflinksGTF_to_CodingQuarryGFF3.py.orig 2016-03-09 01:35:28.000000000 +0100 ++++ CufflinksGTF_to_CodingQuarryGFF3.py 2023-04-10 21:10:51.666438036 +0200 +@@ -5,7 +5,7 @@ + try : + myFile = open(sys.argv[1], 'rU') + except : +- print 'run: \n\npython CufflinksGTF_to_CodingQuarryGFF3.py transcripts.gtf > out.gff3\n' ++ print('run: \n\npython CufflinksGTF_to_CodingQuarryGFF3.py transcripts.gtf > out.gff3\n') + exit() + + number = 0 +@@ -18,8 +18,8 @@ + number += 1 + else : + number = 1 +- print '%s\t%s\texon\t%s\t%s\t%s\t%s\t%s\tID=exon:%s.%i;Parent=%s;' % \ +- (fields[0], fields[1], fields[3], fields[4], fields[5], fields[6], fields[7], details[3], number, details[3]) ++ print('%s\t%s\texon\t%s\t%s\t%s\t%s\t%s\tID=exon:%s.%i;Parent=%s;' % \ ++ (fields[0], fields[1], fields[3], fields[4], fields[5], fields[6], fields[7], details[3], number, details[3])) + IDprev = details[3] + + myFile.close() +--- QuarryFiles/scripts/fastaTranslate.py.orig 2016-03-09 01:35:28.000000000 +0100 ++++ QuarryFiles/scripts/fastaTranslate.py 2023-04-10 21:30:47.355740964 +0200 +@@ -33,7 +33,7 @@ + else : + protein+='*' + i+=3 +- print '>%s' % (record.id) +- print protein ++ print('>%s' % (record.id)) ++ print(protein) + + myFASTA.close() diff --git a/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..8d8017276a60 --- /dev/null +++ b/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'ColabFold' +version = '1.5.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/sokrypton/ColabFold' +description = """Making protein folding accessible to all. Predict proteins structures both in +google colab and on your machine.""" +github_account = 'sokrypton' + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('AlphaFold', '2.3.4', versionsuffix + '-%(name)s'), + ('matplotlib', '3.5.2'), + ('tqdm', '4.64.0'), + ('py3Dmol', '2.0.1.post1'), +] + +use_pip = True + +exts_list = [ + ('colabfold', version, { + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['b3b82e831e241a6ab40f2b0c6d560ac5328c6a0b505a0186c75e397ca1a16477'], + # fix requirement on Python 3.10.x revisions and TensorFlow + 'preinstallopts': r"sed -i 's/^\(python =.*\)<=3.10\"$/\1<3.11\"/;s/flow-cpu/flow/' pyproject.toml &&", + 'use_pip_extras': 'alphafold', + }), +] + +postinstallcmds = [ + # Copy notebooks to installation directory + "mkdir %(installdir)s/notebooks", + "cp AlphaFold2.ipynb ESMFold.ipynb RoseTTAFold.ipynb %(installdir)s/notebooks/", +] + +sanity_check_paths = { + 'files': ['bin/colabfold_batch', 'bin/colabfold_search', 'bin/colabfold_split_msas'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'notebooks'], +} + +sanity_check_commands = [ + "colabfold_batch --help", +] + +sanity_pip_check = True + +modloadmsg = """ +%(name)s notebooks are located in $EBROOTCOLABFOLD/notebooks +""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a.eb b/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a.eb new file mode 100644 index 000000000000..c8ebee84c19f --- /dev/null +++ b/easybuild/easyconfigs/c/ColabFold/ColabFold-1.5.2-foss-2022a.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'ColabFold' +version = '1.5.2' + +homepage = 'https://github.com/sokrypton/ColabFold' +description = """Making protein folding accessible to all. Predict proteins structures both in +google colab and on your machine.""" +github_account = 'sokrypton' + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('AlphaFold', '2.3.4', '-%(name)s'), + ('matplotlib', '3.5.2'), + ('tqdm', '4.64.0'), + ('py3Dmol', '2.0.1.post1'), +] + +use_pip = True + +exts_list = [ + ('colabfold', version, { + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['b3b82e831e241a6ab40f2b0c6d560ac5328c6a0b505a0186c75e397ca1a16477'], + # fix requirement on Python 3.10.x revisions and TensorFlow + 'preinstallopts': r"sed -i 's/^\(python =.*\)<=3.10\"$/\1<3.11\"/;s/flow-cpu/flow/' pyproject.toml &&", + 'use_pip_extras': 'alphafold', + }), +] + +postinstallcmds = [ + # Copy notebooks to installation directory + "mkdir %(installdir)s/notebooks", + "cp AlphaFold2.ipynb ESMFold.ipynb RoseTTAFold.ipynb %(installdir)s/notebooks/", +] + +sanity_check_paths = { + 'files': ['bin/colabfold_batch', 'bin/colabfold_search', 'bin/colabfold_split_msas'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'notebooks'], +} + +sanity_check_commands = [ + "colabfold_batch --help", +] + +sanity_pip_check = True + +modloadmsg = """ +%(name)s notebooks are located in $EBROOTCOLABFOLD/notebooks +""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CopyKAT/CopyKAT-1.1.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/c/CopyKAT/CopyKAT-1.1.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 000000000000..2e0b17c5c7e2 --- /dev/null +++ b/easybuild/easyconfigs/c/CopyKAT/CopyKAT-1.1.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'CopyKAT' +local_commit = 'b795ff7' +version = '1.1.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/navinlabcode/copykat' +description = """CopyKAT: Inference of genomic copy number and subclonal structure of human tumors from + high-throughput single cell RNAseq data""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/navinlabcode/copykat/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['8b4e39591ad81d146873694b8311607bfec88ad57df8daa9244b2e31904193b5'] + +dependencies = [ + ('R', '4.2.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(namelower)s'], +} + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..61e5d8e491f1 --- /dev/null +++ b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'CppUnit' +version = '1.15.1' + +homepage = 'https://freedesktop.org/wiki/Software/cppunit/' + +description = """ + CppUnit is the C++ port of the famous JUnit framework for unit testing. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://dev-www.libreoffice.org/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['89c5c6665337f56fd2db36bc3805a5619709d51fb136e51937072f63fcc717a7'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['lib/libcppunit.a', 'lib/libcppunit.%s' % SHLIB_EXT, + 'lib/pkgconfig/cppunit.pc'], + 'dirs': ['bin', 'include/cppunit', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 000000000000..12a85d600f55 --- /dev/null +++ b/easybuild/easyconfigs/c/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,70 @@ +easyblock = 'PythonBundle' + +name = 'CuPy' +version = '11.4.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://cupy.dev' +description = "CuPy is an open-source array library accelerated with NVIDIA CUDA." + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('pytest', '7.2.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('CUDA', '11.4.1', '', SYSTEM), + ('cuDNN', '8.2.2.26', versionsuffix, SYSTEM), + ('NCCL', '2.10.3', versionsuffix), + ('cuTENSOR', '1.6.1.5', versionsuffix, SYSTEM), + # Adding cuSPARSELt currently makes the build fail. Keeping it around for later versions to pick up. + # ('cuSPARSELt', '0.3.0.3', versionsuffix, SYSTEM), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# A bunch of the tests are failing or are just having problems. +_skip_tests = [ + 'tests/cupyx_tests/scipy_tests', + 'tests/cupyx_tests/distributed_tests', + 'tests/cupyx_tests/tools_tests', + 'tests/example_tests', + 'tests/cupy_tests/testing_tests/test_parameterized.py', + 'tests/cupy_tests/fft_tests/test_fft.py', +] +_ignore_list = ' --ignore='.join(_skip_tests) + +_deselect_tests = [ + 'tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_', + # float16 has too low precision for these tests as they are written + # See https://github.com/easybuilders/easybuild-easyconfigs/pull/17526#issuecomment-1470843170 for details. + 'tests/cupy_tests/linalg_tests/test_product.py::TestProduct', +] +_deselect_list = ' --deselect='.join(_deselect_tests) + +exts_list = [ + ('fastrlock', '0.5', { + 'checksums': ['9ae1a31f6e069b5f0f28ba63c594d0c952065de0a375f7b491d21ebaccc5166f'], + }), + ('cupy', version, { + # Must run tests here since the required version of pytest is a builddep + # Note! test_cudnn and some others will likely fail on T4 GPUs due to out of memory. + 'runtest': 'export CUPY_TEST_GPU_LIMIT=1 CUPY_CACHE_DIR="%%(builddir)s" && ' + 'pytest --ignore=%s --deselect=%s tests' % (_ignore_list, _deselect_list), + 'testinstall': True, + 'checksums': ['03d52b2626e02a3a2b46d714c1cd03e702c8fe33915fcca6ed8de5c539964f49'], + }), +] + +sanity_check_commands = [ + "python -c 'import cupy'", +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..6b168c49490f --- /dev/null +++ b/easybuild/easyconfigs/c/c-ares/c-ares-1.17.2-GCCcore-10.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'c-ares' +version = '1.17.2' + +homepage = 'https://c-ares.haxx.se' +description = "c-ares is a C library for asynchronous DNS requests (including name resolves)" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://c-ares.haxx.se/download/'] +sources = [SOURCE_TAR_GZ] +checksums = ['4803c844ce20ce510ef0eb83f8ea41fa24ecaae9d280c468c582d2bb25b3913d'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['lib/libcares.a', 'lib/libcares.%s' % SHLIB_EXT, 'lib/pkgconfig/libcares.pc'], + 'dirs': ['include', 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..18bf937586b3 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '8.0.1' + +homepage = 'https://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5fd29000a4089934f121eff456101f0a5d09e2a3e89da1d714adf06c4be887cb'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = '--with-zlib ' +configopts += '--with-ssl=$EBROOTOPENSSL ' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/curl'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-13.1.0.eb b/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..10cd7fbe3f24 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-8.0.1-GCCcore-13.1.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '8.0.1' + +homepage = 'https://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5fd29000a4089934f121eff456101f0a5d09e2a3e89da1d714adf06c4be887cb'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = '--with-zlib ' +configopts += '--with-ssl=$EBROOTOPENSSL ' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/curl'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb new file mode 100644 index 000000000000..aab5e755fdf6 --- /dev/null +++ b/easybuild/easyconfigs/c/casacore/casacore-3.4.0-foss-2021b.eb @@ -0,0 +1,48 @@ +# Contribution from Imperial College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'casacore' +version = '3.4.0' + +homepage = 'https://github.com/casacore/casacore' +description = """A suite of C++ libraries for radio astronomy data processing. +The ephemerides data needs to be in DATA_DIR and the location must be specified at runtime. +Thus user's can update them. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/casacore/casacore/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '31f02ad2e26f29bab4a47a2a69e049d7bc511084a0b8263360e6157356f92ae1', # v3.4.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), +] + +dependencies = [ + ('CFITSIO', '3.49'), + ('WCSLIB', '7.11'), + ('HDF5', '1.12.1'), + ('SciPy-bundle', '2021.10'), + ('Boost.Python', '1.77.0'), + ('ncurses', '6.2'), +] + +configopts = ' -DBUILD_PYTHON3=ON -DBUILD_PYTHON=OFF -Wno-dev -DDATA_DIR=%(installdir)s/data ' +configopts += '-DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_MPI=ON ' + +sanity_check_paths = { + 'files': ['lib/libcasa_casa.%s' % SHLIB_EXT, 'lib/libcasa_mirlib.%s' % SHLIB_EXT, + 'lib/libcasa_ms.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/casacore'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..724f8c3da158 --- /dev/null +++ b/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'coverage' +version = '7.2.3' + +homepage = 'https://coverage.readthedocs.io' +description = """ Coverage.py is a tool for measuring code coverage of Python programs. + It monitors your program, noting which parts of the code have been executed, + then analyzes the source to identify code that could have been executed but was not. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d298c2815fa4891edd9abe5ad6e6cb4207104c7dd9fd13aea3fdebf6f9b91259'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/coverage%s' % x for x in ['', '3', '-%(pyshortver)s']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb new file mode 100644 index 000000000000..86ae2b180e92 --- /dev/null +++ b/easybuild/easyconfigs/c/cppzmq/cppzmq-4.9.0.eb @@ -0,0 +1,30 @@ +# ll4strw Lorentz Institute +easyblock = 'CMakeMake' + +name = 'cppzmq' +version = '4.9.0' + +homepage = 'https://github.com/zeromq/cppzmq' +description = "cppzmq is a C++ binding for libzmq." + +toolchain = SYSTEM + +source_urls = ['https://github.com/zeromq/%(name)s/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3fdf5b100206953f674c94d40599bdb3ea255244dcc42fab0d75855ee3645581'] + +builddependencies = [ + ('GCCcore', '11.2.0'), # required for hierarchical module naming scheme + ('binutils', '2.37', '', ('GCCcore', '11.2.0')), + ('CMake', '3.22.1', '', ('GCCcore', '11.2.0')), + ('ZeroMQ', '4.3.4', '', ('GCCcore', '11.2.0')), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['include/zmq.hpp'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.5.2.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.5.2.eb new file mode 100644 index 000000000000..2a9744489075 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.4.1.50-CUDA-11.5.2.eb @@ -0,0 +1,41 @@ +name = 'cuDNN' +version = '8.4.1.50' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# note: cuDNN 8.4.1 is not specific to CUDA 11.6, +# see also https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#cudnn-cuda-hardware-versions +local_short_ver = '.'.join(version.split('.')[:3]) +source_urls = [ + 'https://developer.download.nvidia.com/compute/redist/cudnn/v%s/local_installers/11.6/' % local_short_ver, +] +sources = ['%(namelower)s-linux-%(cudnnarch)s-%(version)s_cuda11.6-archive.tar.xz'] +checksums = [ + { + '%(namelower)s-linux-x86_64-%(version)s_cuda11.6-archive.tar.xz': + 'ec96d2376d81fca42bdd3d4c3d705a99b29a065bab57f920561c763e29c67d01', + '%(namelower)s-linux-ppc64le-%(version)s_cuda11.6-archive.tar.xz': + '8b806cbfdc81352bf76716d1e53b42537665d110c6ffc068be910505c10e1b98', + '%(namelower)s-linux-sbsa-%(version)s_cuda11.6-archive.tar.xz': + '0b1b9fac5b78974e2fdaaa74843db18f636ce8f3d999d62ff2a615b9978fc360', + } +] + +dependencies = [('CUDA', '11.5.2')] + +sanity_check_paths = { + 'files': [ + 'include/cudnn.h', 'lib64/libcudnn_adv_infer_static.a', 'lib64/libcudnn_adv_train_static.a', + 'lib64/libcudnn_cnn_infer_static.a', 'lib64/libcudnn_cnn_train_static.a', + 'lib64/libcudnn_ops_infer_static.a', 'lib64/libcudnn_ops_train_static.a', + 'lib64/libcudnn.%s' % SHLIB_EXT + ], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..5d02753039b9 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +# use http to allow auto-downloading... +source_urls = ['http://download.oracle.com/berkeley-db/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('OpenSSL', '1.1', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20200724-GCC-11.3.0.eb b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20200724-GCC-11.3.0.eb new file mode 100644 index 000000000000..0c8e9e7176c6 --- /dev/null +++ b/easybuild/easyconfigs/d/DBG2OLC/DBG2OLC-20200724-GCC-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CmdCp' + +name = 'DBG2OLC' +version = '20200724' +local_commit = '9514828' + +homepage = 'https://github.com/yechengxi/DBG2OLC' +description = """DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation + Sequencing Technologies""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/yechengxi/DBG2OLC/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['52a05518a377a2bd784265a8dc05c49009f858d4c1c893b4dddbb12106bc0f99'] + +cmds_map = [('.*', "$CXX $CXXFLAGS $LDFLAGS -o DBG2OLC *.cpp")] + +files_to_copy = [(['DBG2OLC'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/DBG2OLC'], + 'dirs': [], +} + +sanity_check_commands = ["DBG2OLC 2>&1 | grep 'For third-gen sequencing: DBG2OLC'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.15.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.15.4-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..686c369b6a73 --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.15.4-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.15.4' + +homepage = 'https://dbus.freedesktop.org/' + +description = """ + D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['bfe53d9e54a4977ec344928521b031af2e97cf78aea58f5d8e2b85ea0a80028b'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('expat', '2.5.0'), +] + +configopts = '--with-systemdsystemunitdir=no ' +# disable documentation +configopts += '--disable-xml-docs --disable-doxygen-docs --disable-ducktype-docs' + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in + ['cleanup-sockets', 'daemon', 'launch', 'monitor', + 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb index 9aa9bdcd1511..71615bf85761 100644 --- a/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DGL/DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb @@ -103,7 +103,10 @@ _copts = [ ] configopts = ' '.join(_copts) -build_shared_libs = True +# Must not build shared libs, DGL uses internal versions of, among others, METIS +# but it doesn't install these internal libraries and simply assumes that everything is +# statically linked. +build_shared_libs = False runtest = 'test' @@ -118,10 +121,9 @@ exts_default_options = { exts_list = [ ('dgl', version, { - 'modulename': False, 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', 'start_dir': 'python', - 'use_pip': False, + 'installopts': '--use-feature=in-tree-build ', 'checksums': ['8d26ebb7ed976665bbf5bbd1792d8e6efb13a8fa16e5eb1efed75e07fb982e04'], }), ] diff --git a/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb new file mode 100644 index 000000000000..9b146a684bac --- /dev/null +++ b/easybuild/easyconfigs/d/DIALOGUE/DIALOGUE-1.0-20230228-foss-2021b-R-4.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'DIALOGUE' +local_commit = '7109f6a' +# see DESCRIPTION file in source to determine version, +# but add date stamp of commit since version is not always bumped +version = '1.0-20230228' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/livnatje/DIALOGUE' +description = """DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to + identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/livnatje/DIALOGUE/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['28a57c61c6854ca4c54114a3067437de6cee0eb1090c46ea45619457affdfb08'] + +dependencies = [ + ('R', '4.2.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.13-foss-2021a.eb b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.13-foss-2021a.eb new file mode 100644 index 000000000000..37b1d866da53 --- /dev/null +++ b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.13-foss-2021a.eb @@ -0,0 +1,29 @@ +# author: Denis Kristak (INUITS) +easyblock = 'PythonBundle' + +name = 'Deprecated' +version = '1.2.13' + +homepage = 'https://github.com/tantale/deprecated' +description = "If you need to mark a function or a method as deprecated, you can use the @deprecated decorator." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), +] + +use_pip = True + +exts_list = [ + ('wrapt', '1.15.0', { + 'checksums': ['d06730c6aed78cee4126234cf2d071e01b44b915e725a6cb439a879ec9754a3a'], + }), + (name, version, { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/DiCE-ML/DiCE-ML-0.9-foss-2022a.eb b/easybuild/easyconfigs/d/DiCE-ML/DiCE-ML-0.9-foss-2022a.eb new file mode 100644 index 000000000000..1103677a97a8 --- /dev/null +++ b/easybuild/easyconfigs/d/DiCE-ML/DiCE-ML-0.9-foss-2022a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'DiCE-ML' +version = '0.9' + +homepage = 'https://interpret.ml/DiCE' +description = "Diverse Counterfactual Explanations (DiCE) for ML" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), + ('scikit-learn', '1.1.2'), + ('tqdm', '4.64.0'), +] + +sources = ['dice_ml-%(version)s.tar.gz'] +checksums = ['0c4c2cb57f2218ba324ef2931304ab42f5f685759688a5898b0eb85b7a25b97a'] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..26007e7a8236 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +name = 'Doxygen' +version = '1.9.7' + +homepage = 'https://www.doxygen.org' +description = """ + Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some + extent D. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +checksums = ['87007641c38e2c392c8596f36711eb97633b984c8430f389e7bcf6323a098d94'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), + ('flex', '2.6.4'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('libiconv', '1.17'), +] + +configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb b/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb new file mode 100644 index 000000000000..54f6a5881f71 --- /dev/null +++ b/easybuild/easyconfigs/d/dask-labextension/dask-labextension-6.0.0-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'dask-labextension' +version = '6.0.0' + +homepage = 'https://github.com/dask/dask-labextension' +description = """This package provides a JupyterLab extension to manage Dask clusters, as well +as embed Dask's dashboard plots directly into JupyterLab panes.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('JupyterLab', '3.5.0'), + ('jupyter-server-proxy', '3.2.2'), + ('dask', '2022.10.0'), +] + +use_pip = True + +exts_list = [ + ('dask_labextension', version, { + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['6b9e6a66fec891d6533314b03a57e121eb9822aaf98c94139c913e7c30212002'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/dask_labextension', 'etc/jupyter', 'share/jupyter'], +} + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.3.1-gompi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.3.1-gompi-2022a.eb new file mode 100644 index 000000000000..2f86924aff49 --- /dev/null +++ b/easybuild/easyconfigs/d/dlb/dlb-3.3.1-gompi-2022a.eb @@ -0,0 +1,35 @@ +# vim: set syntax=python: +easyblock = 'ConfigureMake' + +name = 'dlb' +version = '3.3.1' + +description = """ +DLB is a dynamic library designed to speed up HPC hybrid applications (i.e., +two levels of parallelism) by improving the load balance of the outer level of +parallelism (e.g., MPI) by dynamically redistributing the computational +resources at the inner level of parallelism (e.g., OpenMP). at run time. +""" +homepage = 'https://pm.bsc.es/dlb/' +docurls = ['https://pm.bsc.es/ftp/dlb/doc/user-guide/'] + +toolchain = {'name': 'gompi', 'version': '2022a'} +builddependencies = [('Python', '3.10.4', '-bare')] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pm.bsc.es/ftp/dlb/releases'] + +checksums = ['1b245acad80b03eb83e815fd59dcfc598cfddd899de4504cf6a9572fe5359f40'] + +configopts = '--with-mpi' + +sanity_check_paths = { + 'files': [ + 'bin/dlb', + 'lib/libdlb.a', 'lib/libdlb.%s' % SHLIB_EXT, + 'lib64/libdlb.%s' % SHLIB_EXT + ], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.3.1-iimpi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.3.1-iimpi-2022a.eb new file mode 100644 index 000000000000..7d1205a8d95c --- /dev/null +++ b/easybuild/easyconfigs/d/dlb/dlb-3.3.1-iimpi-2022a.eb @@ -0,0 +1,35 @@ +# vim: set syntax=python: +easyblock = 'ConfigureMake' + +name = 'dlb' +version = '3.3.1' + +description = """ +DLB is a dynamic library designed to speed up HPC hybrid applications (i.e., +two levels of parallelism) by improving the load balance of the outer level of +parallelism (e.g., MPI) by dynamically redistributing the computational +resources at the inner level of parallelism (e.g., OpenMP). at run time. +""" +homepage = 'https://pm.bsc.es/dlb/' +docurls = ['https://pm.bsc.es/ftp/dlb/doc/user-guide/'] + +toolchain = {'name': 'iimpi', 'version': '2022a'} +builddependencies = [('Python', '3.10.4', '-bare')] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pm.bsc.es/ftp/dlb/releases'] + +checksums = ['1b245acad80b03eb83e815fd59dcfc598cfddd899de4504cf6a9572fe5359f40'] + +configopts = '--with-mpi' + +sanity_check_paths = { + 'files': [ + 'bin/dlb', + 'lib/libdlb.a', 'lib/libdlb.%s' % SHLIB_EXT, + 'lib64/libdlb.%s' % SHLIB_EXT + ], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..66e54112889a --- /dev/null +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'double-conversion' +version = '3.3.0' + +homepage = 'https://github.com/google/double-conversion' +description = "Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/google/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['04ec44461850abbf33824da84978043b22554896b552c5fd11a9c5ae4b4d296e'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +separate_build_dir = True + +build_type = 'Release' + +# Build static lib, static lib with -fPIC and shared lib +configopts = [ + '', + '-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_STATIC_LIBRARY_SUFFIX_CXX=_pic.a', + '-DBUILD_SHARED_LIBS=ON' +] + +sanity_check_paths = { + 'files': ['include/double-conversion/%s.h' % h for h in ['bignum', 'cached-powers', 'diy-fp', 'double-conversion', + 'fast-dtoa', 'fixed-dtoa', 'ieee', 'strtod', 'utils']] + + ['lib/libdouble-conversion.%s' % e for e in ['a', SHLIB_EXT]] + ['lib/libdouble-conversion_pic.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb index 6d9cb0dca9b1..fe138398a7a7 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a-CUDA-11.7.0.eb @@ -10,7 +10,7 @@ name = 'ELPA' version = '2022.05.001' versionsuffix = '-CUDA-%(cudaver)s' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications.""" toolchain = {'name': 'foss', 'version': '2022a'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb index 54a1ab0f515c..09d5330ca5b0 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022a.eb @@ -9,7 +9,7 @@ name = 'ELPA' version = '2022.05.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications.""" toolchain = {'name': 'foss', 'version': '2022a'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b-CUDA-12.0.0.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b-CUDA-12.0.0.eb new file mode 100644 index 000000000000..0bf44c8db66a --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b-CUDA-12.0.0.eb @@ -0,0 +1,48 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2022.05.001' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://elpa.mpcdf.mpg.de/' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'}, + {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch': + '1666a133393b3947a80069ae170a51f4d574956f384c01b7018e4b551726a3a2'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.10.8'), + ('Perl', '5.36.0'), +] + +dependencies = [ + ('CUDA', '12.0.0', '', SYSTEM) +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b.eb new file mode 100644 index 000000000000..c9bf9efef08b --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-foss-2022b.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2022.05.001' + +homepage = 'https://elpa.mpcdf.mpg.de/' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'}, + {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch': + '1666a133393b3947a80069ae170a51f4d574956f384c01b7018e4b551726a3a2'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.10.8'), + ('Perl', '5.36.0'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb index 6af27dad5297..2da3666b8597 100644 --- a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022a.eb @@ -9,7 +9,7 @@ name = 'ELPA' version = '2022.05.001' -homepage = 'https://elpa.rzg.mpg.de' +homepage = 'https://elpa.mpcdf.mpg.de' description = """Eigenvalue SoLvers for Petaflop-Applications.""" toolchain = {'name': 'intel', 'version': '2022a'} diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022b.eb new file mode 100644 index 000000000000..473b2dce0331 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2022.05.001-intel-2022b.eb @@ -0,0 +1,47 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2022.05.001' + +homepage = 'https://elpa.mpcdf.mpg.de/' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'intel', 'version': '2022b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix_hardcoded_perl_path.patch'] +checksums = [ + {'elpa-new_release_2022.05.001.tar.gz': '96ff14abe53cc3652ba290a0e309d238147fbbfe054d783efee9890f5f23802d'}, + {'ELPA-2022.05.001_fix_hardcoded_perl_path.patch': + '1666a133393b3947a80069ae170a51f4d574956f384c01b7018e4b551726a3a2'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.10.8'), + ('Perl', '5.36.0'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' +# If the build is running in a batch job, make sure Intel libmpi does +# not try to use Slurm to run the MPI_THREAD test code that ELPA's +# configure is running without "mpirun". +preconfigopts += 'unset SLURM_JOBID && unset SLURM_NODELIST && unset I_MPI_PMI_LIBRARY && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b-PEXSI.eb new file mode 100644 index 000000000000..347ad480808b --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b-PEXSI.eb @@ -0,0 +1,39 @@ +name = 'ELSI' +version = '2.5.0' +versionsuffix = '-PEXSI' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/02/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix-compiler-detection.patch'] +checksums = [ + 'f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f', + '4ffb0bb91fa385ffc4884fe0bb3a8b6ef69107aef9e6f0e8c4f5f19eaf7c0fb5', +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.3.2'), + ('CMake', '3.15.3'), +] + +dependencies = [ + ('ELPA', '2019.11.001'), + # SLEPc and internal PEXSI can't coexist due to conflicting dependencies + # ('SLEPc', '3.12.2', '-Python-3.7.4'), +] + +build_internal_pexsi = True + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b.eb new file mode 100644 index 000000000000..00a54e827fd6 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-foss-2019b.eb @@ -0,0 +1,38 @@ +name = 'ELSI' +version = '2.5.0' + +homepage = 'https://wordpress.elsi-interchange.org/' +description = """ELSI provides and enhances scalable, open-source software library solutions for + electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. + ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. + The ELSI infrastructure should also be useful for other challenging eigenvalue problems. +""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/02/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_fix-compiler-detection.patch'] +checksums = [ + 'f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f', + '4ffb0bb91fa385ffc4884fe0bb3a8b6ef69107aef9e6f0e8c4f5f19eaf7c0fb5', +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.3.2'), + ('CMake', '3.15.3'), +] + +dependencies = [ + ('ELPA', '2019.11.001'), + ('SLEPc', '3.12.2', '-Python-3.7.4'), +] + +# SLEPc and internal PEXSI can't coexist due to conflicting dependencies +build_internal_pexsi = False + +runtest = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b-PEXSI.eb index 7a3d6a93e714..84704deb0c43 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b-PEXSI.eb @@ -14,7 +14,11 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/02/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f'] +patches = ['%(name)s-%(version)s_fix-compiler-detection.patch'] +checksums = [ + 'f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f', + '4ffb0bb91fa385ffc4884fe0bb3a8b6ef69107aef9e6f0e8c4f5f19eaf7c0fb5', +] builddependencies = [ ('flex', '2.6.4'), diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b.eb index ca508d490f83..4ba1e4b7a8a5 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0-intel-2019b.eb @@ -13,7 +13,11 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/02/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f'] +patches = ['%(name)s-%(version)s_fix-compiler-detection.patch'] +checksums = [ + 'f4d77c4291341c9708ab8070dc4ec683577b3556e7d9f214370d626dc6a4753f', + '4ffb0bb91fa385ffc4884fe0bb3a8b6ef69107aef9e6f0e8c4f5f19eaf7c0fb5', +] builddependencies = [ ('flex', '2.6.4'), diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0_fix-compiler-detection.patch b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0_fix-compiler-detection.patch new file mode 100644 index 000000000000..c61708a48f97 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.5.0_fix-compiler-detection.patch @@ -0,0 +1,40 @@ +Let CMake search for the compilers and only fail if they are not found. +See https://gitlab.com/elsi_project/elsi_interface/-/merge_requests/304 + +Author: Alexander Grund (TU Dresden) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index b8d22e53..f1570a8e 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -67,14 +67,18 @@ SET(INC_PATHS "" CACHE STRING "List of include directories") + SET(LIBS "" CACHE STRING "List of external libraries to be linked against") + + ### Compilers ### +-IF(NOT DEFINED CMAKE_Fortran_COMPILER) ++INCLUDE(CheckLanguage) ++ ++CHECK_LANGUAGE(Fortran) ++IF(NOT CMAKE_Fortran_COMPILER) + MESSAGE(FATAL_ERROR "${MAGENTA}Fortran compiler must be set${COLORRESET}") + ELSE() + MESSAGE(STATUS "${GREEN}Fortran compiler${COLORRESET}: ${CMAKE_Fortran_COMPILER}") + ENABLE_LANGUAGE(Fortran) + ENDIF() + IF(ENABLE_PEXSI OR ENABLE_C_TESTS OR ELPA2_KERNEL STREQUAL "AVX512" OR ELPA2_KERNEL STREQUAL "AVX2" OR ELPA2_KERNEL STREQUAL "AVX") +- IF(NOT DEFINED CMAKE_C_COMPILER) ++ CHECK_LANGUAGE(C) ++ IF(NOT CMAKE_C_COMPILER) + MESSAGE(FATAL_ERROR "${MAGENTA}C compiler must be set${COLORRESET}") + ELSE() + MESSAGE(STATUS "${GREEN}C compiler${COLORRESET}: ${CMAKE_C_COMPILER}") +@@ -82,7 +86,8 @@ IF(ENABLE_PEXSI OR ENABLE_C_TESTS OR ELPA2_KERNEL STREQUAL "AVX512" OR ELPA2_KER + ENDIF() + ENDIF() + IF(ENABLE_PEXSI) +- IF(NOT DEFINED CMAKE_CXX_COMPILER) ++ CHECK_LANGUAGE(CXX) ++ IF(NOT CMAKE_CXX_COMPILER) + MESSAGE(FATAL_ERROR "${MAGENTA}C++ compiler must be set${COLORRESET}") + ELSE() + MESSAGE(STATUS "${GREEN}C++ compiler${COLORRESET}: ${CMAKE_CXX_COMPILER}") diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb index 332df2352b0b..68020a6e2914 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-foss-2020b-PEXSI.eb @@ -16,11 +16,13 @@ source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11 sources = [SOURCELOWER_TAR_GZ] patches = [ 'pexsi-1.2.0-mpi30.patch', + '%(name)s-%(version)s_fix-compiler-detection.patch', 'ELSI-2.7.1_bison_3.7_compat.patch', ] checksums = [ 'e43fc12b4954ecd70813fcb45aaef39779f7d9bb5270bbc7246e88d92c8b1dc4', # elsi-2.6.4.tar.gz 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch + '43b7112e4b0e9e3da2d353947bf3a0b3d1773463d8af831ef335a0e073e95a37', # ELSI-2.6.4_fix-compiler-detection.patch '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb', # ELSI-2.7.1_bison_3.7_compat.patch ] diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb index 800d33b16dc2..ff84be63e3a4 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4-intel-2020b-PEXSI.eb @@ -16,11 +16,13 @@ source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2020/11 sources = [SOURCELOWER_TAR_GZ] patches = [ 'pexsi-1.2.0-mpi30.patch', + '%(name)s-%(version)s_fix-compiler-detection.patch', 'ELSI-2.7.1_bison_3.7_compat.patch', ] checksums = [ 'e43fc12b4954ecd70813fcb45aaef39779f7d9bb5270bbc7246e88d92c8b1dc4', # elsi-2.6.4.tar.gz 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch + '43b7112e4b0e9e3da2d353947bf3a0b3d1773463d8af831ef335a0e073e95a37', # ELSI-2.6.4_fix-compiler-detection.patch '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb', # ELSI-2.7.1_bison_3.7_compat.patch ] diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4_fix-compiler-detection.patch b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4_fix-compiler-detection.patch new file mode 100644 index 000000000000..5e931749a787 --- /dev/null +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.6.4_fix-compiler-detection.patch @@ -0,0 +1,36 @@ +Let CMake search for the compilers and only fail if they are not found. +See https://gitlab.com/elsi_project/elsi_interface/-/merge_requests/304 + +Author: Alexander Grund (TU Dresden) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 3f016ec7..9aaf8395 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -55,18 +55,23 @@ SET(INC_PATHS "" CACHE STRING "List of include directories") + SET(LIBS "" CACHE STRING "List of external libraries to be linked against") + + ### Compilers ### +-IF(NOT DEFINED CMAKE_Fortran_COMPILER) ++INCLUDE(CheckLanguage) ++ ++CHECK_LANGUAGE(Fortran) ++IF(NOT CMAKE_Fortran_COMPILER) + MESSAGE(FATAL_ERROR "${MAGENTA}Fortran compiler must be set${COLORRESET}") + ENDIF() + ENABLE_LANGUAGE(Fortran) + +-IF(NOT DEFINED CMAKE_C_COMPILER) ++CHECK_LANGUAGE(C) ++IF(NOT CMAKE_C_COMPILER) + MESSAGE(FATAL_ERROR "${MAGENTA}C compiler must be set${COLORRESET}") + ENDIF() + ENABLE_LANGUAGE(C) + + IF(ENABLE_PEXSI) +- IF(NOT DEFINED CMAKE_CXX_COMPILER) ++ CHECK_LANGUAGE(CXX) ++ IF(NOT CMAKE_CXX_COMPILER) + MESSAGE(FATAL_ERROR "${MAGENTA}C++ compiler must be set${COLORRESET}") + ENDIF() + ENABLE_LANGUAGE(CXX) diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb index 97218cbf6a8c..1995ff511e03 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-foss-2021a-PEXSI.eb @@ -16,11 +16,13 @@ source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2021/03 sources = [SOURCELOWER_TAR_GZ] patches = [ 'pexsi-1.2.0-mpi30.patch', + '%(name)s-2.6.4_fix-compiler-detection.patch', 'ELSI-2.7.1_bison_3.7_compat.patch', ] checksums = [ '4a70b6047c39f4e0fd5eca1b2543bfa600acb8305a05ccaaf823ca045f8a4e4d', # elsi-2.7.1.tar.gz 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch + '43b7112e4b0e9e3da2d353947bf3a0b3d1773463d8af831ef335a0e073e95a37', # ELSI-2.6.4_fix-compiler-detection.patch '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb', # ELSI-2.7.1_bison_3.7_compat.patch ] diff --git a/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb index 94759abacfcd..6e3baf0eb4cd 100644 --- a/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb +++ b/easybuild/easyconfigs/e/ELSI/ELSI-2.7.1-intel-2021a-PEXSI.eb @@ -16,11 +16,13 @@ source_urls = ['http://wordpress.elsi-interchange.org/wp-content/uploads/2021/03 sources = [SOURCELOWER_TAR_GZ] patches = [ 'pexsi-1.2.0-mpi30.patch', + '%(name)s-2.6.4_fix-compiler-detection.patch', 'ELSI-2.7.1_bison_3.7_compat.patch', ] checksums = [ '4a70b6047c39f4e0fd5eca1b2543bfa600acb8305a05ccaaf823ca045f8a4e4d', # elsi-2.7.1.tar.gz 'd5580de710cee652c27622f167a10933f792546481d9c08d62f452885cb63abb', # pexsi-1.2.0-mpi30.patch + '43b7112e4b0e9e3da2d353947bf3a0b3d1773463d8af831ef335a0e073e95a37', # ELSI-2.6.4_fix-compiler-detection.patch '986f95c2eb22c8a8bef13357a10242dcf0a0fac562c88bdc9bdf46cc6e7a1edb', # ELSI-2.7.1_bison_3.7_compat.patch ] diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 000000000000..a8901cbb3d13 --- /dev/null +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,55 @@ +easyblock = 'CMakeMake' + +name = 'ESPResSo' +version = '4.2.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://espressomd.org/wordpress' +description = """A software package for performing and analyzing scientific Molecular Dynamics simulations.""" + +source_urls = ['https://github.com/espressomd/espresso/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f7264d78fe1fd7774b89972fe10d5b15d2e9d620d406158dab90df5df0b9f255'] + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'usempi': True, 'pic': True} + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('CUDA', '11.3.1', '', SYSTEM), + ('SciPy-bundle', '2021.05'), + ('Boost.MPI', '1.76.0'), + ('HDF5', '1.10.7'), + ('Mesa', '21.1.1'), + ('GSL', '2.7'), + ('IPython', '7.25.0'), + ('Pint', '0.20.1'), +] + +configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON' + +runtest = 'check_unit_tests && make check_python' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +_binaries = ['ipypresso', 'pypresso'] +_libs = [ + 'Espresso_config', 'Espresso_core', 'Espresso_script_interface', 'Espresso_shapes', + '_init', 'analyze', 'code_info', 'cuda_init', 'electrokinetics', 'galilei', + 'integrate', 'interactions', 'lb', 'particle_data', 'polymer', 'profiler', + 'script_interface', 'system', 'thermostat', 'utils', 'version', +] + +_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + [_lib_path + '/%s.' % x + SHLIB_EXT for x in _libs], + 'dirs': ['bin', 'lib'] +} + +sanity_check_commands = ['pypresso -h', 'ipypresso -h'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/e/EZC3D/EZC3D-1.5.2-foss-2022a.eb b/easybuild/easyconfigs/e/EZC3D/EZC3D-1.5.2-foss-2022a.eb new file mode 100644 index 000000000000..e7880604adc1 --- /dev/null +++ b/easybuild/easyconfigs/e/EZC3D/EZC3D-1.5.2-foss-2022a.eb @@ -0,0 +1,39 @@ +easyblock = "CMakePythonPackage" + +name = 'EZC3D' +version = '1.5.2' + +homepage = 'https://pyomeca.github.io/Documentation/ezc3d/index.html' +description = """EZC3D is an easy to use reader, modifier and writer for C3D format files. It is +written en C++ with proper binders for Python and MATLAB/Octave scripting +langages.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'pyomeca' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['Release_%(version)s.tar.gz'] +checksums = ['469c2089c0f885c9dd994bb02d70939da1ec2ddd37ea353964aafa8a5b2d7165'] + +builddependencies = { + ('binutils', '2.38'), + ('CMake', '3.24.3'), + ('SWIG', '4.0.2'), +} + +dependencies = { + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +} + +# enable Python bindings +_py_install_dir = "%(installdir)s/lib/python%(pyshortver)s/site-packages/%(namelower)s" +configopts = "-DBINDER_PYTHON3=ON " +configopts += "-DPYTHON_INSTALL_PREFIX=%s" % _py_install_dir + +sanity_check_paths = { + 'files': ['lib/libezc3d.%s' % SHLIB_EXT], + 'dirs': ['include/ezc3d', _py_install_dir], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.1.eb new file mode 100644 index 000000000000..8d9ac53bb937 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.7.1.eb @@ -0,0 +1,45 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.7.1' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/76/4b/b7a88e791cce0d79db9f2319ab07c79584815ca9e497d178c39fa4621b8d/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/10/72/391eb5bde081da67fef0a59625ce7cf4939176416aed299ef55923e422b4/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/32/1a/e7c851db23ffb0fc5c3cc9c255318d533f642c86eff2c3c33e0ab063a449/', + +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + {'easybuild-framework-4.7.1.tar.gz': 'ad3d95c2b11f895666d83cda3422e785261ecb9d14e7c3e0c9cef427b7404d6b'}, + {'easybuild-easyblocks-4.7.1.tar.gz': '8c383dc4d02784e5ab610cec2df58c19ff9c1b7c03bb7585788ced1646e394e8'}, + {'easybuild-easyconfigs-4.7.1.tar.gz': '58c70e7e4a8958f932e4e7abab0194198a8f9baf19915bfa5191b431f3f1a864'}, +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..dfd909ce7791 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.4.0-GCCcore-12.3.0.eb @@ -0,0 +1,21 @@ +name = 'Eigen' +version = '3.4.0' + +homepage = 'https://eigen.tuxfamily.org' +description = """Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, + and related algorithms.""" + +# only includes header files, but requires CMake so using non-system toolchain +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.com/libeigen/eigen/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b4c198460eba6f28d34894e3a5710998818515104d6e74e5cc331ce31e46e626'] + +# using CMake built with GCCcore to avoid relying on the system compiler to build it +builddependencies = [ + ('binutils', '2.40'), # to make CMake compiler health check pass on old systems + ('CMake', '3.26.3'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb b/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb new file mode 100644 index 000000000000..90325d9c67c9 --- /dev/null +++ b/easybuild/easyconfigs/e/Evcxr-REPL/Evcxr-REPL-0.14.2-GCCcore-12.2.0-Rust-1.65.0.eb @@ -0,0 +1,460 @@ +easyblock = 'Cargo' + +name = 'Evcxr-REPL' +version = '0.14.2' +local_rustver = '1.65.0' +versionsuffix = '-Rust-' + local_rustver + +homepage = 'https://github.com/evcxr' +description = "A Rust REPL (Read-Eval-Print loop) built using the evcxr evaluation context." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +crates = [ + ('evcxr_repl', version), + ('evcxr', version), + ('addr2line', '0.19.0'), + ('adler', '1.0.2'), + ('always-assert', '0.1.2'), + ('ansi_term', '0.12.1'), + ('anyhow', '1.0.68'), + ('anymap', '1.0.0-beta.2'), + ('ariadne', '0.1.5'), + ('arrayvec', '0.7.2'), + ('atty', '0.2.14'), + ('autocfg', '1.1.0'), + ('backtrace', '0.3.67'), + ('bitflags', '1.3.2'), + ('camino', '1.1.1'), + ('cargo-platform', '0.1.2'), + ('cargo_metadata', '0.15.2'), + ('cc', '1.0.78'), + ('cfg-if', '1.0.0'), + ('chalk-derive', '0.88.0'), + ('chalk-ir', '0.88.0'), + ('chalk-recursive', '0.88.0'), + ('chalk-solve', '0.88.0'), + ('clap', '2.34.0'), + ('clipboard-win', '4.4.2'), + ('colored', '2.0.0'), + ('countme', '3.0.1'), + ('cov-mark', '2.0.0-pre.1'), + ('crossbeam-channel', '0.5.6'), + ('crossbeam-deque', '0.8.2'), + ('crossbeam-epoch', '0.9.13'), + ('crossbeam-utils', '0.8.14'), + ('ctrlc', '3.2.4'), + ('dashmap', '5.4.0'), + ('dirs', '4.0.0'), + ('dirs-next', '2.0.0'), + ('dirs-sys', '0.3.7'), + ('dirs-sys-next', '0.1.2'), + ('dissimilar', '1.0.5'), + ('dot', '0.1.4'), + ('drop_bomb', '0.1.5'), + ('either', '1.8.0'), + ('ena', '0.14.0'), + ('endian-type', '0.1.2'), + ('errno', '0.2.8'), + ('errno-dragonfly', '0.1.2'), + ('error-code', '2.3.1'), + ('evcxr_input', '1.0.0'), + ('fastrand', '1.8.0'), + ('fd-lock', '3.0.8'), + ('filetime', '0.2.19'), + ('fixedbitset', '0.2.0'), + ('form_urlencoded', '1.1.0'), + ('fsevent-sys', '4.1.0'), + ('fst', '0.4.7'), + ('getrandom', '0.2.8'), + ('gimli', '0.27.0'), + ('hashbrown', '0.12.3'), + ('heck', '0.3.3'), + ('hermit-abi', '0.1.19'), + ('hermit-abi', '0.2.6'), + ('hkalbasi-rustc-ap-rustc_abi', '0.0.20221221'), + ('hkalbasi-rustc-ap-rustc_index', '0.0.20221221'), + ('home', '0.5.4'), + ('idna', '0.3.0'), + ('indexmap', '1.9.2'), + ('inotify', '0.9.6'), + ('inotify-sys', '0.1.5'), + ('instant', '0.1.12'), + ('io-lifetimes', '1.0.3'), + ('itertools', '0.10.5'), + ('itoa', '1.0.5'), + ('jod-thread', '0.1.2'), + ('json', '0.12.4'), + ('kqueue', '1.0.7'), + ('kqueue-sys', '1.0.3'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.139'), + ('libloading', '0.7.4'), + ('libmimalloc-sys', '0.1.28'), + ('linux-raw-sys', '0.1.4'), + ('lock_api', '0.4.9'), + ('log', '0.4.17'), + ('memchr', 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'49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'}, + {'walkdir-2.3.2.tar.gz': '808cf2735cd4b6866113f648b791c6adc5714537bc222d9347bb203386ffda56'}, + {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'}, + {'which-4.3.0.tar.gz': '1c831fbbee9e129a8cf93e7747a82da9d95ba8e16621cae60ec2cdc849bacb7b'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-util-0.1.5.tar.gz': '70ec6ce85bb158151cae5e5c87f95a8e97d2c0c4b001223f33a334e3ce5de178'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-sys-0.42.0.tar.gz': '5a3e1820f08b8513f676f7ab6c1f99ff312fb97b553d30ff4dd86f9f15728aa7'}, + {'windows_aarch64_gnullvm-0.42.0.tar.gz': '41d2aa71f6f0cbe00ae5167d90ef3cfe66527d6f613ca78ac8024c3ccab9a19e'}, + {'windows_aarch64_msvc-0.42.0.tar.gz': 'dd0f252f5a35cac83d6311b2e795981f5ee6e67eb1f9a7f64eb4500fbc4dcdb4'}, + {'windows_i686_gnu-0.42.0.tar.gz': 'fbeae19f6716841636c28d695375df17562ca208b2b7d0dc47635a50ae6c5de7'}, + {'windows_i686_msvc-0.42.0.tar.gz': '84c12f65daa39dd2babe6e442988fc329d6243fdce47d7d2d155b8d874862246'}, + {'windows_x86_64_gnu-0.42.0.tar.gz': 'bf7b1b21b5362cbc318f686150e5bcea75ecedc74dd157d874d754a2ca44b0ed'}, + {'windows_x86_64_gnullvm-0.42.0.tar.gz': '09d525d2ba30eeb3297665bd434a54297e4170c7f1a44cad4ef58095b4cd2028'}, + {'windows_x86_64_msvc-0.42.0.tar.gz': 'f40009d85759725a34da6d89a94e63d7bdc50a862acf0dbc7c8e488f1edcb6f5'}, + {'yansi-0.5.1.tar.gz': '09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec'}, +] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Rust', local_rustver), +] + +sanity_check_paths = { + 'files': ['bin/evcxr'], + 'dirs': [], +} + +sanity_check_commands = ["evcxr --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..d1d7854b68d6 --- /dev/null +++ b/easybuild/easyconfigs/e/elfutils/elfutils-0.189-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'elfutils' +version = '0.189' + +homepage = 'https://elfutils.org/' + +description = """ + The elfutils project provides libraries and tools for ELF files + and DWARF data. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://sourceware.org/elfutils/ftp/%(version)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['39bd8f1a338e2b7cd4abc3ff11a0eddc6e690f69578a57478d8179b4148708c8'] + +builddependencies = [ + ('M4', '1.4.19'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('binutils', '2.40'), + ('bzip2', '1.0.8'), + ('libarchive', '3.6.2'), + ('XZ', '5.4.2'), + ('zstd', '1.5.5'), +] + +configopts = "--disable-debuginfod --disable-libdebuginfod" + +sanity_check_paths = { + 'files': ['bin/eu-elfcmp', 'include/dwarf.h', 'lib/libelf.%s' % SHLIB_EXT], + 'dirs': [] +} + +sanity_check_commands = ["eu-elfcmp --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/expat/expat-2.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/expat/expat-2.5.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..5cca3ac204ef --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.5.0' + +homepage = 'https://libexpat.github.io' + +description = """Expat is an XML parser library written in C. It is a stream-oriented parser +in which an application registers handlers for things the parser might find +in the XML document (like start tags).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libexpat/libexpat/releases/download/R_%s/' % version.replace('.', '_')] +sources = [SOURCE_TAR_BZ2] +checksums = ['6f0e6e01f7b30025fa05c85fdad1e5d0ec7fd35d9f61b22f34998de11969ff67'] + +builddependencies = [('binutils', '2.40')] + +# Since expat 2.2.6, docbook2X is needed to produce manpage of xmlwf. +# Docbook2X needs XML-Parser and XML-Parser needs expat. +# -> circular dependency. "--without-docbook" breaks this circle. +configopts = ['--without-docbook'] + +sanity_check_paths = { + 'files': ['include/expat.h', 'lib/libexpat.a', 'lib/libexpat.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-11.2.0.eb new file mode 100644 index 000000000000..ddc7db52078b --- /dev/null +++ b/easybuild/easyconfigs/f/FASTA/FASTA-36.3.8i-GCC-11.2.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'FASTA' +version = '36.3.8i' +local_version_date = '14-Nov-2020' + +homepage = 'http://fasta.bioch.virginia.edu' +description = """The FASTA programs find regions of local or global (new) similarity between +protein or DNA sequences, either by searching Protein or DNA databases, or by identifying +local duplications within a sequence.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/wrpearson/fasta36/archive/'] +sources = ['v%%(version)s_%s.tar.gz' % local_version_date] +checksums = ['b4b1c3c9be6beebcbaf4215368e159d69255e34c0bdbc84affa10cdb473ce008'] + +buildopts = '-C ./src -f ../make/Makefile.linux_sse2 all' + +files_to_copy = ['bin', 'conf', 'data', 'doc', 'FASTA_LIST', 'misc', 'README', 'seq', 'sql', 'test'] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s fasta%(version_major)s fasta"] + +sanity_check_paths = { + 'files': ['FASTA_LIST', 'README'] + ['bin/fasta', 'bin/map_db'] + + ['bin/%s%%(version_major)s' % x for x in ['fasta', 'fastm', 'fastx', 'ggsearch', 'lalign', 'tfastf', + 'tfasts', 'tfasty', 'fastf', 'fasts', 'fasty', 'glsearch', + 'ssearch', 'tfastm', 'tfastx']], + 'dirs': ['conf', 'data', 'doc', 'misc', 'seq', 'sql', 'test'] +} + +sanity_check_commands = ["fasta --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb new file mode 100644 index 000000000000..8589f7ecedc9 --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-11.3.0.eb @@ -0,0 +1,95 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'Bundle' + +name = 'FASTX-Toolkit' +version = '0.0.14' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +default_easyblock = 'ConfigureMake' + +dependencies = [ + ('GDGraph', '1.56'), + ('Perl', '5.34.1'), +] + +components = [ + ('libgtextutils', '0.7', { + 'source_urls': ['https://github.com/agordon/libgtextutils/releases/download/%(version)s/'], + 'sources': [SOURCE_TAR_GZ], + 'patches': ['libgtextutils-%(version)s_fix-bool.patch'], + 'checksums': [ + '792e0ea3c96ffe3ad65617a104b7dc50684932bc96d2adab501c952fd65c3e4a', # libgtextutils-0.7.tar.gz + 'bb16a4fd86c2eb12215d8780b09f0898771a73e53889a015e2351f2d737c9a00', # libgtextutils-0.7_fix-bool.patch + ], + 'start_dir': 'libgtextutils-%(version)s', + }), + (name, version, { + 'source_urls': ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'], + 'sources': ['fastx_toolkit-%(version)s.tar.bz2'], + 'checksums': ['9e1f00c4c9f286be59ac0e07ddb7504f3b6433c93c5c7941d6e3208306ff5806'], + 'start_dir': 'fastx_toolkit-%(version)s', + 'preconfigopts': "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ", + 'configopts': 'CXXFLAGS="$CXXFLAGS -Wno-implicit-fallthrough"', + }), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('PerlIO::gzip', '0.20', { + 'source_tmpl': 'PerlIO-gzip-0.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/'], + 'checksums': ['4848679a3f201e3f3b0c5f6f9526e602af52923ffa471a2a3657db786bd3bdc5'], + }), +] + +fix_perl_shebang_for = ['bin/*.pl'] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/' +} + +sanity_check_paths = { + 'files': + ['bin/fastx_%s' % x for x in + ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in + ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in + ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', + 'quality_trimmer', 'masker']] + + ['lib/libgtextutils.%s' % SHLIB_EXT, 'lib/libgtextutils.a'], + 'dirs': [] +} + +sanity_check_commands = [ + 'fasta_clipping_histogram.pl', + 'fasta_formatter -h', + 'fastq_masker -h | grep "FASTX Toolkit %(version)s"', + 'fastq_quality_boxplot_graph.sh', + 'fastx_barcode_splitter.pl --help | grep "Barcode Splitter, by Assaf Gordon (gordon@cshl.edu), 11sep2008"', + 'fastx_clipper -h | grep "FASTX Toolkit %(version)s"', + 'fastx_nucleotide_distribution_graph.sh', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FHI-aims/FHI-aims-221103-intel-2022a.eb b/easybuild/easyconfigs/f/FHI-aims/FHI-aims-221103-intel-2022a.eb new file mode 100644 index 000000000000..7e9bb34bb356 --- /dev/null +++ b/easybuild/easyconfigs/f/FHI-aims/FHI-aims-221103-intel-2022a.eb @@ -0,0 +1,57 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Dugan Witherick (University of Warwick) +# Updated to 210716_3 +# J. Sassmannshausen (Imperial College London/UK) +## +easyblock = 'CMakeMake' + +name = 'FHI-aims' +version = '221103' + +homepage = 'https://fhi-aims.org/' +description = """FHI-aims is an efficient, accurate all-electron, +full-potential electronic structure code package for computational molecular +and materials science (non-periodic and periodic systems). The code supports +DFT (semilocal and hybrid) and many-body perturbation theory. FHI-aims is +particularly efficient for molecular systems and nanostructures, while +maintaining high numerical accuracy for all production tasks. Production +calculations handle up to several thousand atoms and can efficiently use (ten) +thousands of cores. +""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'opt': True, 'precise': True} + +download_instructions = """ +The source code must be downloaded manually from the FHI-aims club +(https://fhi-aims.org/get-the-code-menu/login). +Access to the FHI-aims club requires a valid license and registration. +Details on available license options and how to register to access +FHI-aims club may be found at: +https://fhi-aims.org/get-the-code-menu/get-the-code """ + +sources = ['%(namelower)s.%(version)s.tgz'] +checksums = ['1905147a15968b6b719a4f5d9495a958df648d3ccee58f5012734be5d6727749'] + +builddependencies = [('CMake', '3.24.3')] + +configopts = ' -DCMAKE_Fortran_COMPILER="$MPIF90" ' +configopts += ' -DLIBS="mkl_scalapack_lp64 mkl_blacs_intelmpi_lp64 mkl_intel_lp64 mkl_sequential mkl_core" ' +configopts += ' -DLIB_PATHS="$CMAKE_LIBRARY_PATH" ' +configopts += ' -DCMAKE_C_FLAGS="$CFLAGS -ip" ' +configopts += ' -DCMAKE_Fortran_FLAGS="$FFLAGS -ip" ' +configopts += ' -DFortran_MIN_FLAGS="-O0 -fp-model precise" ' +configopts += ' -DTARGET_NAME="aims.x" ' + +postinstallcmds = ["cp -ar %(builddir)s/%(namelower)s.%(version)s/{CHANGELOG.md,doc,external} %(installdir)s/", + "cp -ar %(builddir)s/%(namelower)s.%(version)s/{regression_tests,species_defaults} %(installdir)s/", + "cp -ar %(builddir)s/%(namelower)s.%(version)s/{testcases,utilities} %(installdir)s/"] + +sanity_check_paths = { + 'files': ['bin/aims.x'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/f/FLAC/FLAC-1.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..6b89c621af0e --- /dev/null +++ b/easybuild/easyconfigs/f/FLAC/FLAC-1.4.2-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FLAC' +version = '1.4.2' + +homepage = 'https://xiph.org/flac/' +description = """FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning +that audio is compressed in FLAC without any loss in quality.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/flac/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['e322d58a1f48d23d9dd38f432672865f6f79e73a6f9cc5a5f57fcaa83eb5a8e4'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['bin/flac', 'lib/libFLAC.a', 'lib/libFLAC++.a', + 'lib/libFLAC.%s' % SHLIB_EXT, 'lib/libFLAC++.%s' % SHLIB_EXT], + 'dirs': ['include/FLAC', 'include/FLAC++'], +} + +sanity_check_commands = ["flac --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-foss-2021b.eb similarity index 65% rename from easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb rename to easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-foss-2021b.eb index 8b3d55e165dc..493b0f97e4f1 100644 --- a/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4-foss-2021b.eb @@ -10,22 +10,34 @@ description = """FLINT (Fast Library for Number Theory) is a C library in suppor factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'foss', 'version': '2021b'} toolchainopts = {'pic': True} source_urls = ['https://www.flintlib.org'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['61df92ea8c8e9dc692d46c71d7f50aaa09a33d4ba08d02a1784730a445e5e4be'] +patches = [ + '%(name)s-%(version)s_find_flexiblas.patch', +] +checksums = [ + {'flint-2.8.4.tar.gz': '61df92ea8c8e9dc692d46c71d7f50aaa09a33d4ba08d02a1784730a445e5e4be'}, + {'FLINT-2.8.4_find_flexiblas.patch': '35a3db14646daf584449f2b9c6880b66e7b082a665eba56234230610bab77c6e'}, +] builddependencies = [ ('CMake', '3.22.1'), + ('Python', '3.9.6'), ] dependencies = [ ('GMP', '6.2.1'), ('MPFR', '4.1.0'), + ('NTL', '11.5.1'), ] +configopts = '-DWITH_NTL=on -DBUILD_TESTING=yes' + +runtest = 'test' + sanity_check_paths = { 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], 'dirs': ['include'], diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4_find_flexiblas.patch b/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4_find_flexiblas.patch new file mode 100644 index 000000000000..54412d05b236 --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.8.4_find_flexiblas.patch @@ -0,0 +1,23 @@ +Use FlexiBLAS when available + +Åke Sandgren, 2023-05-03 +diff -ru flint-2.8.4.orig/CMake/FindCBLAS.cmake flint-2.8.4/CMake/FindCBLAS.cmake +--- flint-2.8.4.orig/CMake/FindCBLAS.cmake 2021-11-17 18:43:50.000000000 +0100 ++++ flint-2.8.4/CMake/FindCBLAS.cmake 2023-05-03 09:29:36.599062848 +0200 +@@ -11,13 +11,13 @@ + find_path(CBLAS_INCLUDE_DIRS NAMES cblas.h + HINTS CBLAS_ROOT ENV CBLAS_ROOT + PATHS ${INCLUDE_INSTALL_DIR} ${CMAKE_INSTALL_PREFIX}/include +- PATH_SUFFIXES openblas cblas blis ++ PATH_SUFFIXES flexiblas openblas cblas blis + ) + +-find_library(CBLAS_LIBRARIES NAMES accelerate openblas cblas blas blis ++find_library(CBLAS_LIBRARIES NAMES accelerate flexiblas openblas cblas blas blis + HINTS CBLAS_ROOT ENV CBLAS_ROOT + PATHS ${LIB_INSTALL_DIR} ${CMAKE_INSTALL_PREFIX}/lib +- PATH_SUFFIXES openblas cblas blis ++ PATH_SUFFIXES flexiblas openblas cblas blis + ) + + include(FindPackageHandleStandardArgs) diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022a.eb similarity index 79% rename from easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb rename to easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022a.eb index 90131d5e4c4d..8d6bb6cc6fbb 100644 --- a/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/f/FLINT/FLINT-2.9.0-gfbf-2022a.eb @@ -10,22 +10,30 @@ description = """FLINT (Fast Library for Number Theory) is a C library in suppor factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" -toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchain = {'name': 'gfbf', 'version': '2022a'} toolchainopts = {'pic': True} source_urls = ['https://www.flintlib.org'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['2fc090d51033c93208e6c10d406397a53c983ae5343b958eb25f72a57a4ce76a'] +patches = [ + '%(name)s-2.8.4_find_flexiblas.patch', +] builddependencies = [ ('CMake', '3.23.1'), + ('Python', '3.10.4'), ] dependencies = [ ('GMP', '6.2.1'), ('MPFR', '4.1.0'), + ('NTL', '11.5.1'), ] +configopts = '-DWITH_NTL=on -DBUILD_TESTING=yes' + +runtest = 'test' + sanity_check_paths = { 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], 'dirs': ['include'], diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..856159422b14 --- /dev/null +++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MesonNinja' + +name = 'FUSE' +version = '3.14.1' + +homepage = 'https://github.com/libfuse/libfuse' +description = "The reference implementation of the Linux FUSE (Filesystem in Userspace) interface" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/libfuse/libfuse/releases/download/fuse-%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['126919d72b46b3e0eb58a9c6933a2a50c36f2ea69f61fe9e78bdba9f463ffa20'] + +builddependencies = [ + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('binutils', '2.38'), +] + +# -Dutils=True only works as root +configopts = '-Dutils=False' + +sanity_check_paths = { + 'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT, + 'lib64/pkgconfig/fuse%(version_major)s.pc'], + 'dirs': ['include/fuse%(version_major)s'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..1be427492064 --- /dev/null +++ b/easybuild/easyconfigs/f/FUSE/FUSE-3.14.1-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MesonNinja' + +name = 'FUSE' +version = '3.14.1' + +homepage = 'https://github.com/libfuse/libfuse' +description = "The reference implementation of the Linux FUSE (Filesystem in Userspace) interface" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/libfuse/libfuse/releases/download/fuse-%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['126919d72b46b3e0eb58a9c6933a2a50c36f2ea69f61fe9e78bdba9f463ffa20'] + +builddependencies = [ + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('binutils', '2.39') +] + +# -Dutils=True only works as root +configopts = '-Dutils=False' + +sanity_check_paths = { + 'files': ['lib64/libfuse%%(version_major)s.%s' % SHLIB_EXT, + 'lib64/pkgconfig/fuse%(version_major)s.pc'], + 'dirs': ['include/fuse%(version_major)s'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb index 11318dc50bb2..2d4bc28f2bdd 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.2.0.eb @@ -27,6 +27,11 @@ cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s - files_to_copy = [(['FastTree'], 'bin')] +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + sanity_check_paths = { 'files': ['bin/FastTree'], 'dirs': [], diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb index ad1c23f20f58..fdcb06c67f31 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-10.3.0.eb @@ -27,6 +27,11 @@ cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s - files_to_copy = [(['FastTree'], 'bin')] +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + sanity_check_paths = { 'files': ['bin/FastTree'], 'dirs': [], diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb index 51f3e343ef96..9bbfa3f435b4 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.2.0.eb @@ -27,6 +27,11 @@ cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s - files_to_copy = [(['FastTree'], 'bin')] +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + sanity_check_paths = { 'files': ['bin/FastTree'], 'dirs': [], diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb index a79c7a054dab..c1bb41ac734a 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb @@ -27,6 +27,11 @@ cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s - files_to_copy = [(['FastTree'], 'bin')] +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + sanity_check_paths = { 'files': ['bin/FastTree'], 'dirs': [], diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.9.2-foss-2022b.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.9.2-foss-2022b.eb new file mode 100644 index 000000000000..024b51efc9f7 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.9.2-foss-2022b.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Fiona' +version = '1.9.2' + +homepage = 'https://github.com/Toblerity/Fiona' +description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data +in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, +mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using +multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS +packages such as pyproj, Rtree, and Shapely.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('GDAL', '3.6.2'), + ('Shapely', '2.0.1'), # optional for 'calc' extras +] + +use_pip = True + +exts_list = [ + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + (name, version, { + 'use_pip_extras': 'calc', + 'checksums': ['f9263c5f97206bf2eb2c010d52e8ffc54e96886b0e698badde25ff109b32952a'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["fio --help"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/Flask/Flask-2.2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/Flask/Flask-2.2.3-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..26e22ef4b44a --- /dev/null +++ b/easybuild/easyconfigs/f/Flask/Flask-2.2.3-GCCcore-12.2.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'Flask' +version = '2.2.3' + +homepage = 'https://www.palletsprojects.com/p/flask/' +description = """ +Flask is a lightweight WSGI web application framework. It is designed to make +getting started quick and easy, with the ability to scale up to complex +applications. +This module includes the Flask extensions: Flask-Cors""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +dependencies = [ + ('Python', '3.10.8'), +] + +builddependencies = [('binutils', '2.39')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('itsdangerous', '2.1.2', { + 'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'], + }), + ('Werkzeug', version, { + 'checksums': ['2e1ccc9417d4da358b9de6f174e3ac094391ea1d4fbef2d667865d819dfd0afe'], + }), + ('asgiref', '3.6.0', { + 'checksums': ['9567dfe7bd8d3c8c892227827c41cce860b368104c3431da67a0c5a65a949506'], + }), + (name, version, { + 'checksums': ['7eb373984bf1c770023fce9db164ed0c3353cd0b53f130f4693da0ca756a2e6d'], + }), + ('Flask-Cors', '3.0.10', { + 'checksums': ['b60839393f3b84a0f3746f6cdca56c1ad7426aa738b70d6c61375857823181de'], + }), + ('cachelib', '0.10.2', { + 'checksums': ['593faeee62a7c037d50fc835617a01b887503f972fb52b188ae7e50e9cb69740'], + }), + ('Flask-Session', '0.4.0', { + 'checksums': ['c9ed54321fa8c4ca0132ffd3369582759eda7252fb4b3bee480e690d1ba41f46'], + }), +] + +sanity_check_paths = { + 'files': ['bin/flask'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['flask --version'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb new file mode 100644 index 000000000000..f2205d273fba --- /dev/null +++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1-foss-2022a.eb @@ -0,0 +1,105 @@ +easyblock = 'Tarball' + +name = 'FunGAP' +version = '1.1.1' + +homepage = 'https://github.com/CompSynBioLab-KoreaUniv/FunGAP' +description = "Fungal Genome Annotation Pipeline using evidence-based gene model evaluation." + +toolchain = {'name': 'foss', 'version': '2022a'} + +# Tag v1.1.1 points to an old commit still in v1.1.0 +# pull correct sources from specific commit +_commit = '924f3ba080f98cbf181b0b21601e095619479ce6' + +source_urls = ['https://github.com/CompSynBioLab-KoreaUniv/FunGAP/archive'] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] +patches = [ + 'FunGAP-%(version)s_fix-snap-detection.patch', + 'FunGAP-%(version)s_relax-dependency-checks.patch', + 'FunGAP-%(version)s_replace-deprecated-pa-repeatmodeler.patch', + 'FunGAP-%(version)s_fix-maker-exes.patch', + 'FunGAP-%(version)s_fix-augustus-calls-in-runbreaker.patch', +] +checksums = [ + {'FunGAP-1.1.1.tar.gz': '3d827c4b11452afdd51b71766e0e3193b7efad31db4536606115f2cac0b964c8'}, + {'FunGAP-1.1.1_fix-snap-detection.patch': 'f782224ce186e1e2d8953898122b79d616f8a749b00ec662ec5a3fa1903550fa'}, + {'FunGAP-1.1.1_relax-dependency-checks.patch': '73f9ae2a20cf03c34f852642a28d3b7e9858250f653ff1e711c3c9a56ae2fd77'}, + {'FunGAP-1.1.1_replace-deprecated-pa-repeatmodeler.patch': + 'c528aab74a070d6eedc9ff2097b6149e8d36759b9ff93c46302994179a38a774'}, + {'FunGAP-1.1.1_fix-maker-exes.patch': 'de344cf45dad047ab46a17462e19ce0789a89071c1484cbdedd9d898f9601bd0'}, + {'FunGAP-1.1.1_fix-augustus-calls-in-runbreaker.patch': + '150b6f79f95d0c8abece42231c5dcedf8610a811db9cc63ac6cc047f0dcfdc64'}, +] + +dependencies = [ + ('Python', '3.10.4'), + ('Perl', '5.34.1'), + ('AUGUSTUS', '3.5.0'), + ('BamTools', '2.5.2'), + ('bcbio-gff', '0.7.0'), + ('BRAKER', '2.1.6'), + ('BUSCO', '5.4.5'), + ('HISAT2', '2.2.1'), + ('MAKER', '3.01.04'), + ('matplotlib', '3.5.2'), + ('networkx', '2.8.4'), + ('PfamScan', '1.6'), + ('RepeatModeler', '2.0.4'), + ('SAMtools', '1.16.1'), + ('SNAP-HMM', '20221022'), + ('Trinity', '2.15.1'), + ('wget', '1.21.3'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('markdown2', '2.4.8', { + 'checksums': ['90475aca3d9c8e7df6d70c51de5bbbe9edf7fcf6a380bd1044d321500f5445da'], + }), +] + +# FunGAP needs the Pfam database (280 MB download, 1.5 GB on disk) +# if it's already available in your system change _pfam_db_dir to its location +_pfam_db_dir = '%(installdir)s/db' +_pfam_db_url = 'https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release' +_pfam_db_install_cmds = [ + "mkdir -p %s" % _pfam_db_dir, + "wget -P %s %s/{Pfam-A.hmm.gz,Pfam-A.hmm.dat.gz,active_site.dat.gz}" % (_pfam_db_dir, _pfam_db_url), + "gzip -d %s/*.gz" % _pfam_db_dir, + "hmmpress %s/Pfam-A.hmm" % _pfam_db_dir, +] + +postinstallcmds = [ + # install Pfam DB if missing + "if [ ! -f %s/Pfam-A.hmm ]; then %s; fi" % (_pfam_db_dir, " && ".join(_pfam_db_install_cmds)), + # execute set_dependencies.py, which creates configuration file and runs some quick tests + ("cd %%(installdir)s && ./set_dependencies.py --pfam_db_path %s --genemark_path $EBROOTGENEMARKMINET " + "--maker_path $EBROOTMAKER/bin --snap_path $EBROOTSNAPMINHMM/bin" % _pfam_db_dir), +] + +sanity_check_paths = { + 'files': ['fungap.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': ['', 'lib/python%(pyshortver)s/site-packages'] +} + +modextravars = { + 'FUNGAP_DIR': '%(installdir)s', +} + +sanity_check_commands = [ + ('fungap.py', '--help'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-augustus-calls-in-runbreaker.patch b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-augustus-calls-in-runbreaker.patch new file mode 100644 index 000000000000..a245df16275a --- /dev/null +++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-augustus-calls-in-runbreaker.patch @@ -0,0 +1,54 @@ +Set paths to AUGUSTUS installation preferably from its environment variables +Fix location of getAnnoFastaFromJoingenes.py script from AUGUSTUS +see https://github.com/CompSynBioLab-KoreaUniv/FunGAP/pull/98 +author: Alex Domingo (Vrije Universirteit Brussel) +--- run_braker.py.orig 2023-04-03 12:07:35.178272000 +0200 ++++ run_braker.py 2023-04-03 12:24:48.713953000 +0200 +@@ -124,8 +124,19 @@ + logger_time.debug('START: BRAKER') + + if not os.path.exists(gff3_braker): +- augustus_config_path = os.path.join( +- os.path.dirname(D_CONF['AUGUSTUS_PATH']), '../config') ++ augustus_bin_path = os.environ[ ++ 'AUGUSTUS_BIN_PATH' ++ ] or os.path.dirname(D_CONF['AUGUSTUS_PATH']) ++ augustus_config_path = os.environ[ ++ 'AUGUSTUS_CONFIG_PATH' ++ ] or os.path.join( ++ os.path.dirname(D_CONF['AUGUSTUS_PATH']), '../config' ++ ) ++ augustus_scripts_path = os.environ[ ++ 'AUGUSTUS_SCRIPTS_PATH' ++ ] or os.path.join( ++ os.path.dirname(D_CONF['AUGUSTUS_PATH']), '../scripts' ++ ) + config_species = os.path.join( + augustus_config_path, 'species', prefix) + species = prefix +@@ -140,7 +151,6 @@ + bamtools_path = os.path.dirname(D_CONF['BAMTOOLS_PATH']) + genemark_path = os.path.dirname(D_CONF['GENEMARK_PATH']) + samtools_path = os.path.dirname(D_CONF['SAMTOOLS_PATH']) +- augustus_scripts_path = os.path.dirname(D_CONF['AUGUSTUS_PATH']) + working_dir = os.path.join(output_dir, prefix) + if not os.path.exists(working_dir): + os.mkdir(working_dir) +@@ -153,7 +163,7 @@ + braker_bin, fungus_flag, num_cores, adjusted_assembly, + bam_file, species, augustus_config_path, bamtools_path, + genemark_path, samtools_path, working_dir, +- translation_table, augustus_scripts_path, log_braker)) ++ translation_table, augustus_bin_path, log_braker)) + logger_txt.debug('[Run] %s', command1) + os.system(command1) + +@@ -165,7 +175,7 @@ + + augustus_dir = os.path.dirname(D_CONF['AUGUSTUS_PATH']) + get_anno_script = os.path.join( +- augustus_dir, 'getAnnoFastaFromJoingenes.py') ++ augustus_scripts_path, 'getAnnoFastaFromJoingenes.py') + if not os.path.exists(get_anno_script): + get_anno_script = os.path.join( + augustus_dir, diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-maker-exes.patch b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-maker-exes.patch new file mode 100644 index 000000000000..b172ca04d47f --- /dev/null +++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-maker-exes.patch @@ -0,0 +1,20 @@ +The paths to MAKER executables set by MAKER are already correct, avoid +tampering with them. +author: Alex Domingo (Vrije Universiteit Brussel) +--- run_maker.py.orig 2023-03-21 09:19:05.057679000 +0100 ++++ run_maker.py 2023-03-21 09:19:49.143408491 +0100 +@@ -463,14 +463,6 @@ + replace('maker_opts.ctl', 'protein_pass=0', 'protein_pass=1') + replace('maker_opts.ctl', 'rm_pass=0', 'rm_pass=1') + +- # Program paths +- for program in [ +- 'makeblastdb', 'blastn', 'blastx', 'tblastx', 'RepeatMasker', +- 'exonerate', 'snap', 'augustus', 'tRNAscan-SE', 'snoscan']: +- replace('maker_exe.ctl', '{}='.format(program), '{}={}'.format( +- program, os.path.join(os.path.dirname(maker_bin), program) +- )) +- + # Last run, keep_preds=1 + if version == '4': + replace('maker_opts.ctl', 'keep_preds=0', 'keep_preds=1') diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-snap-detection.patch b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-snap-detection.patch new file mode 100644 index 000000000000..c8dd7ab62621 --- /dev/null +++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_fix-snap-detection.patch @@ -0,0 +1,61 @@ +Fix detection of fathom, forge and hmm-assembler.pl, which are not part of MAKER but SNAP +see https://github.com/CompSynBioLab-KoreaUniv/FunGAP/pull/97 +author: Alex Domingo (Vrije Universiteit Brussel) +--- set_dependencies.py.orig 2023-03-16 15:27:00.506475000 +0100 ++++ set_dependencies.py 2023-03-16 15:31:31.102674857 +0100 +@@ -44,6 +44,10 @@ + help='Maker bin path' + ) + parser.add_argument( ++ '-s', '--snap_path', nargs=1, required=True, ++ help='SNAP-HMM bin path' ++ ) ++ parser.add_argument( + '-r', '--with_repeat_modeler', nargs='?', default='', + help='User-defined RepeatModeler bin path' + ) +@@ -76,6 +80,7 @@ + pfam_db_path = os.path.abspath(args.pfam_db_path[0]) + i_genemark_path = os.path.abspath(args.genemark_path[0]) + i_maker_path = os.path.abspath(args.maker_path[0]) ++ i_snap_path = os.path.abspath(args.snap_path[0]) + if args.with_repeat_modeler: + with_repeat_modeler = os.path.abspath(args.with_repeat_modeler) + else: +@@ -104,8 +109,9 @@ + pfam_scan_path, blastp_path, blastn_path, blastx_path, + makeblastdb_path, samtools_path, bamtools_path, augustus_path + ) = get_path( +- i_genemark_path, i_maker_path, with_repeat_modeler, with_augustus, +- with_hisat2, with_trinity, with_braker, with_busco, with_pfam_scan ++ i_genemark_path, i_maker_path, i_snap_path, with_repeat_modeler, ++ with_augustus, with_hisat2, with_trinity, with_braker, with_busco, ++ with_pfam_scan + ) + check_working( + genemark_path, gmhmme3_path, probuild_path, build_database_path, +@@ -159,8 +165,9 @@ + + + def get_path( +- i_genemark_path, i_maker_path, with_repeat_modeler, with_augustus, +- with_hisat2, with_trinity, with_braker, with_busco, with_pfam_scan): ++ i_genemark_path, i_maker_path, i_snap_path, with_repeat_modeler, ++ with_augustus, with_hisat2, with_trinity, with_braker, with_busco, ++ with_pfam_scan): + '''Get path''' + print('\n** Checking the installed locations of dependencies **\n') + +@@ -198,9 +205,9 @@ + gff3_merge_path = check_binary('Maker', i_maker_path, 'gff3_merge') + fasta_merge_path = check_binary('Maker', i_maker_path, 'fasta_merge') + maker2zff_path = check_binary('Maker', i_maker_path, 'maker2zff') +- fathom_path = check_binary('Snap', i_maker_path, 'fathom') +- forge_path = check_binary('Snap', i_maker_path, 'forge') +- hmm_assembler_path = check_binary('Snap', i_maker_path, 'hmm-assembler.pl') ++ fathom_path = check_binary('Snap', i_snap_path, 'fathom') ++ forge_path = check_binary('Snap', i_snap_path, 'forge') ++ hmm_assembler_path = check_binary('Snap', i_snap_path, 'hmm-assembler.pl') + build_database_path = check_binary( + 'RepeatModeler (BuildDatabase)', with_repeat_modeler, 'BuildDatabase', + ) diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_relax-dependency-checks.patch b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_relax-dependency-checks.patch new file mode 100644 index 000000000000..68d88fe47b24 --- /dev/null +++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_relax-dependency-checks.patch @@ -0,0 +1,29 @@ +Disable too strict check on version of AUGUSTUS and the GeneMark key in the +home directory of the user +author: Alex Domingo (Vrije Universiteit Brusel) +--- set_dependencies.py.orig 2023-03-16 15:50:03.802522000 +0100 ++++ set_dependencies.py 2023-03-16 15:50:28.562603082 +0100 +@@ -284,15 +284,15 @@ + check_working_internal(samtools_path, [samtools_path, '--help']) + check_working_internal(bamtools_path, [bamtools_path, '--help']) + check_working_internal(augustus_path, [augustus_path, '--help']) +- check_augustus_version(augustus_path) ++ # check_augustus_version(augustus_path) + +- # For GeneMark, check the .gm_key +- home_path = os.path.expanduser('~') +- if not os.path.exists(os.path.join(home_path, '.gm_key')): +- sys.exit( +- '\n[ERROR] You do not have .gm_key in your home directory.\n' +- 'Check https://wiki.gacrc.uga.edu/wiki/GeneMark' +- ) ++ # # For GeneMark, check the .gm_key ++ # home_path = os.path.expanduser('~') ++ # if not os.path.exists(os.path.join(home_path, '.gm_key')): ++ # sys.exit( ++ # '\n[ERROR] You do not have .gm_key in your home directory.\n' ++ # 'Check https://wiki.gacrc.uga.edu/wiki/GeneMark' ++ # ) + + def check_augustus_version(augustus_path): + '''Check Augustus version 3.3.3''' diff --git a/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_replace-deprecated-pa-repeatmodeler.patch b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_replace-deprecated-pa-repeatmodeler.patch new file mode 100644 index 000000000000..8d75c3a8ae6f --- /dev/null +++ b/easybuild/easyconfigs/f/FunGAP/FunGAP-1.1.1_replace-deprecated-pa-repeatmodeler.patch @@ -0,0 +1,22 @@ +Replace deprecated -pa option in newer versions of RepeatModeler with -threads +author: Alex Domingo (Vrije Universiteit Brussel) +--- run_repeat_modeler.py.orig 2023-03-17 09:23:21.857374000 +0100 ++++ run_repeat_modeler.py 2023-03-17 09:24:17.655942000 +0100 +@@ -73,7 +73,7 @@ + + # BuildDatabase -name Choanephora_cucurbitarum + # ../Choanephora_cucurbitarum_assembly.fna +- # RepeatModeler -database Choanephora_cucurbitarum -pa 25 ++ # RepeatModeler -database Choanephora_cucurbitarum -threads 25 + + # Get repeat model + repeat_lib = os.path.join(output_dir, '*', 'consensi.fa.classified') +@@ -89,7 +89,7 @@ + os.system(command1) + + log_file2 = os.path.join(log_dir, 'repeat_modeler.log') +- command2 = '{} -database {} -pa {} > {} 2>&1'.format( ++ command2 = '{} -database {} -threads {} > {} 2>&1'.format( + repeatmodeler_bin, genome_assembly, num_cores, log_file2 + ) + logger_txt.debug('[Run] %s', command2) diff --git a/easybuild/easyconfigs/f/fio/fio-3.34-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fio/fio-3.34-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..0b7184963e51 --- /dev/null +++ b/easybuild/easyconfigs/f/fio/fio-3.34-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'fio' +version = '3.34' + +homepage = 'https://github.com/axboe/fio' +docurls = 'https://fio.readthedocs.io/en/latest/index.html' +description = 'Flexible I/O tester' + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'axboe' +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['42ea28c78d269c4cc111b7516213f4d4b32986797a710b0ff364232cc7a3a0b7'] + +builddependencies = [ + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['bin', 'man', 'share'], +} + +sanity_check_commands = ['fio -h'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..a1d5afb9dbdf --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'https://github.com/westes/flex' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('help2man', '1.49.3'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.40', '', SYSTEM), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.1.0.eb b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..6d11a9f3e06d --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.4-GCCcore-13.1.0.eb @@ -0,0 +1,34 @@ +name = 'flex' +version = '2.6.4' + +homepage = 'https://github.com/westes/flex' + +description = """ + Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, + sometimes called a tokenizer, is a program which recognizes lexical patterns + in text. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/westes/flex/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87aae032bf07c26f85ac0ed3250998c37621d95f8bd748b31f15b33c45ee995'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('help2man', '1.49.3'), + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.40', '', SYSTEM), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +# glibc 2.26 requires _GNU_SOURCE defined to expose reallocarray in the correct +# header, see https://github.com/westes/flex/issues/241 +preconfigopts = 'export CPPFLAGS="$CPPFLAGS -D_GNU_SOURCE" && ' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..ad80d0891f90 --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-10.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '10.0.0' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['4943cb165f3f587f26da834d3056ee8733c397e024145ca7d2a8a96bb71ac281'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/fmt/fmt-9.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fmt/fmt-9.1.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..cfaa82feaea2 --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-9.1.0-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '9.1.0' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['cceb4cb9366e18a5742128cb3524ce5f50e88b476f1e54737a47ffdf4df4c996'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39') +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.4.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..0f9d2c522158 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.4.0-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.4.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['3c0bcb915d9b180a97edaebd011b7a1de54583a838644dcd42bb0ea0c6f3eaec'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('X11', '20221110'), + ('Mesa', '22.2.4'), + ('libGLU', '9.0.2'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.%s" ' % SHLIB_EXT +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.%s" ' % SHLIB_EXT +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb new file mode 100644 index 000000000000..78068a53cc2e --- /dev/null +++ b/easybuild/easyconfigs/f/funannotate/funannotate-1.8.13-foss-2021b.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'funannotate' +version = '1.8.13' + +homepage = 'https://funannotate.readthedocs.io' +description = """funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work + with higher eukaryotes)""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Biopython', '1.79'), + ('GOATOOLS', '1.3.1'), + ('matplotlib', '3.4.3'), + ('scikit-learn', '1.0.1'), + ('Seaborn', '0.11.2'), +] + +use_pip = True + +exts_list = [ + ('distro', '1.8.0', { + 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + }), + ('natsort', '8.3.1', { + 'checksums': ['517595492dde570a4fd6b6a76f644440c1ba51e2338c8a671d7f0475fda8f9fd'], + }), + (name, version, { + 'checksums': ['40819741bcb38ef3a410a242cc5f172cb0e0083570daddfe5807fb6bc0c3c384'], + }), +] + +sanity_check_paths = { + 'files': ['bin/funannotate'], + 'dirs': [], +} + +sanity_check_commands = ["funannotate --help 2>&1 | grep 'Usage:[ ]*funannotate'"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2-gompi-2022a.eb b/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2-gompi-2022a.eb new file mode 100644 index 000000000000..2d4407c36992 --- /dev/null +++ b/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2-gompi-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'GATB-Core' +version = '1.4.2' + +homepage = 'https://gatb.inria.fr/software/gatb-core' +description = """GATB-Core is a high-performance and low memory footprint C++ library that provides a set of highly + efficient algorithms to analyse NGS data sets""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/GATB/gatb-core/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch'] +checksums = [ + {'v1.4.2.tar.gz': '824c84a3712973746b977a9d49923fd499021a894225231100eaad1a66e9742d'}, + {'GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch': + '938ff686e1fc8170b8ef4a73c1c0af059eb3eb76a6251b44a3dfddf991e05c63'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('HDF5', '1.12.2'), +] + +start_dir = 'gatb-core' + +preconfigopts = "rm -r %(start_dir)s/thirdparty/{boost,hdf5} && " + +sanity_check_paths = { + 'files': ['bin/dbginfo', 'bin/leon', 'lib/libgatbcore.a'], + 'dirs': ['include/gatb'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch b/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch new file mode 100644 index 000000000000..e9e4b86b9c29 --- /dev/null +++ b/easybuild/easyconfigs/g/GATB-Core/GATB-Core-1.4.2_no-thirdparty-boost-hdf5.patch @@ -0,0 +1,232 @@ +don't use vendored boost/hdf5 from gatb-core/thirdparty +author: Kenneth Hoste (HPC-UGent) +diff -ru gatb-core-1.4.2.orig/gatb-core/CMakeLists.txt gatb-core-1.4.2/gatb-core/CMakeLists.txt +--- gatb-core-1.4.2.orig/gatb-core/CMakeLists.txt 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/CMakeLists.txt 2023-03-31 21:25:42.862864064 +0200 +@@ -209,7 +209,7 @@ + set (gatb-core-includes ${PROJECT_BINARY_DIR}/include ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE} ${PROJECT_SOURCE_DIR}/src ${PROJECT_SOURCE_DIR}/thirdparty ${gatb-core-extra-libraries-inc}) + + # We define the libraries used for linking binary based on gatb core +-set (gatb-core-libraries gatbcore-static dl pthread z hdf5-static ${gatb-core-extra-libraries}) ++set (gatb-core-libraries gatbcore-static dl pthread z hdf5 ${gatb-core-extra-libraries}) + + # We define the directory where to find cmake helpers + set (gatb-core-cmake ${CMAKE_MODULE_PATH}) +@@ -252,12 +252,6 @@ + ADD_SUBDIRECTORY(thirdparty) + + ################################################################################ +-# DEPENDENCIES +-################################################################################ +-# we must be sure that hdf5 is built and installed before building gatb-core +-ADD_DEPENDENCIES (gatbcore-static hdf5-static hdf5_postbuild) +- +-################################################################################ + # DOCUMENTATION GENERATION + ################################################################################ + IF (EXISTS "${PROJECT_SOURCE_DIR}/doc") +@@ -286,7 +280,6 @@ + INSTALL (FILES ${PROJECT_SOURCE_DIR}/doc/misc/README.txt DESTINATION . OPTIONAL) + INSTALL (FILES ${PROJECT_SOURCE_DIR}/LICENCE DESTINATION . OPTIONAL) + INSTALL (FILES ${PROJECT_SOURCE_DIR}/THIRDPARTIES.md DESTINATION . OPTIONAL) +- INSTALL (DIRECTORY ${PROJECT_SOURCE_DIR}/thirdparty/boost DESTINATION ./include) + ENDIF() + + ################################################################################ +--- gatb-core-1.4.2.orig/gatb-core/thirdparty/CMakeLists.txt 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/thirdparty/CMakeLists.txt 2023-03-31 14:39:11.999034862 +0200 +@@ -1,54 +1,3 @@ +-################################################################################ +-# HDF5 GENERATION +-################################################################################ +- +-#SET (HDF5_ENABLE_THREADSAFE ON) +-#SET (H5_HAVE_THREADSAFE 1) +- +-########## MOMENTARY DEACTIVATED => CRASH ON MACOS TO BE INVESTIGATED ########## +-SET (HDF5_BUILD_TOOLS ON CACHE BOOL "Build HDF5 Tools") +-#SET (CMAKE_EXE_LINKER_FLAGS "-lpthread -lz") +- +-SET (HDF5_EXTERNALLY_CONFIGURED ON) +- +-#SET (HDF5_INSTALL_BIN_DIR ${PROJECT_BINARY_DIR}/bin/${CMAKE_BUILD_TYPE}) +-#SET (HDF5_INSTALL_LIB_DIR ${PROJECT_BINARY_DIR}/lib/${CMAKE_BUILD_TYPE}) +-SET (HDF5_INSTALL_BIN_DIR bin) +-SET (HDF5_INSTALL_LIB_DIR lib) +- +-SET (HDF5_INSTALL_INCLUDE_DIR ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5) +-SET (HDF5_INSTALL_DATA_DIR ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE}) +-SET (HDF5_INSTALL_CMAKE_DIR ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE}) +- +-IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE) +- SET (HDF5_EXPORTED_TARGETS "gatb-hdf5") +-ENDIF() +- +-IF (NOT DEFINED GATB_CORE_EXCLUDE_HDF5_ZLIB) +- OPTION (HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" ON) +-ENDIF() +- +-# We don't want warnings from HDF5 compilation +-set (COMPILE_DEFINITIONS "${COMPILE_DEFINITIONS} -w") +-add_definitions (${COMPILE_DEFINITIONS}) +- +-# add HDF5 generation +-ADD_SUBDIRECTORY (hdf5) +- +-# We add a custom target for copying header files. +-add_custom_target (hdf5_postbuild ALL) +- +-# We build the output directory +-add_custom_command (TARGET hdf5_postbuild POST_BUILD COMMAND ${CMAKE_COMMAND} -E make_directory ${HDF5_INSTALL_INCLUDE_DIR}) +- +-# We define all the header files to be copied +-file (GLOB headerfiles ${PROJECT_SOURCE_DIR}/thirdparty/hdf5/src/*.h ${PROJECT_BINARY_DIR}/thirdparty/hdf5/H5pubconf.h) +- +-# We copy each header file +-foreach (header ${headerfiles}) +- add_custom_command (TARGET hdf5_postbuild POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_if_different ${header} ${HDF5_INSTALL_INCLUDE_DIR} ) +-endforeach() +- + # include other smaller libraries (json, Boophf) + + add_custom_target (thirdparty_copy ALL) +@@ -63,7 +12,6 @@ + # INSTALL + ################################################################################ + IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE) +- INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5 DESTINATION include) + INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/json DESTINATION include) + INSTALL (DIRECTORY ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/BooPHF DESTINATION include) + ENDIF () +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/LargeInt.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/LargeInt.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/LargeInt.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/LargeInt.hpp 2023-03-31 10:40:57.005450131 +0200 +@@ -35,7 +35,7 @@ + #include + #include + #include +-#include ++#include + + #include + #include +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt128.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt128.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt128.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt128.hpp 2023-03-31 10:40:57.005450131 +0200 +@@ -33,7 +33,7 @@ + /********************************************************************************/ + + #include +-#include ++#include + + #include + #include +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt16.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt16.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt16.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt16.hpp 2023-03-31 10:40:57.005450131 +0200 +@@ -31,7 +31,7 @@ + #include + #include + #include +-#include ++#include + + /********************************************************************************/ + namespace gatb { +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt32.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt32.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt32.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt32.hpp 2023-03-31 10:40:57.006450171 +0200 +@@ -31,7 +31,7 @@ + #include + #include + #include +-#include ++#include + + /********************************************************************************/ + namespace gatb { +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt64.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt64.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt64.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt64.hpp 2023-03-31 10:40:57.006450171 +0200 +@@ -31,7 +31,7 @@ + #include + #include + #include +-#include ++#include + + extern const unsigned char revcomp_4NT[]; + extern const unsigned char comp_NT []; +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt8.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt8.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/math/NativeInt8.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/math/NativeInt8.hpp 2023-03-31 10:40:57.006450171 +0200 +@@ -31,7 +31,7 @@ + #include + #include + #include +-#include ++#include + + /********************************************************************************/ + namespace gatb { +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/misc/api/Abundance.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/misc/api/Abundance.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/misc/api/Abundance.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/misc/api/Abundance.hpp 2023-03-31 10:40:57.006450171 +0200 +@@ -31,7 +31,7 @@ + /********************************************************************************/ + + #include +-#include ++#include + + /********************************************************************************/ + namespace gatb { +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp 2023-03-31 10:40:57.007450212 +0200 +@@ -28,7 +28,7 @@ + + #include + #include +-#include ++#include + + /********************************************************************************/ + namespace gatb { +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp 2023-03-31 10:40:57.007450212 +0200 +@@ -40,7 +40,7 @@ + #include + #include + #include +-#include ++#include + + /********************************************************************************/ + namespace gatb { +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp 2023-03-31 10:40:57.008450252 +0200 +@@ -40,7 +40,7 @@ + #include + #include + #include +-#include ++#include + + /********************************************************************************/ + namespace gatb { +diff -ru gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp +--- gatb-core-1.4.2.orig/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp 2020-04-12 23:15:34.000000000 +0200 ++++ gatb-core-1.4.2/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp 2023-03-31 10:40:57.008450252 +0200 +@@ -33,7 +33,7 @@ + #include + #include + #include +-#include ++#include + #include + + /********************************************************************************/ diff --git a/easybuild/easyconfigs/g/GCC/GCC-12.3.0.eb b/easybuild/easyconfigs/g/GCC/GCC-12.3.0.eb new file mode 100644 index 000000000000..e2701264c4c5 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-12.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '12.3.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain) + ('binutils', '2.40', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-13.1.0.eb b/easybuild/easyconfigs/g/GCC/GCC-13.1.0.eb new file mode 100644 index 000000000000..8bf33a423ce0 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-13.1.0.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '13.1.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of binutils (built with system toolchain) + ('binutils', '2.40', '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb new file mode 100644 index 000000000000..45270c7b7f81 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb @@ -0,0 +1,63 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '12.3.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://sourceware.org/pub/gcc/releases/gcc-%(version)s', # fallback URL for GCC + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.2.1.tar.bz2', + 'mpfr-4.2.0.tar.bz2', + 'mpc-1.3.1.tar.gz', + 'isl-0.26.tar.bz2', + 'newlib-4.3.0.20230120.tar.gz', + {'download_filename': '93e0090.tar.gz', 'filename': 'nvptx-tools-20230122.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', +] +checksums = [ + {'gcc-12.3.0.tar.gz': '11275aa7bb34cd8ab101d01b341015499f8d9466342a2574ece93f954d92273b'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.2.0.tar.bz2': '691db39178e36fc460c046591e4b0f2a52c8f2b3ee6d750cc2eab25f1eaa999d'}, + {'mpc-1.3.1.tar.gz': 'ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'}, + {'isl-0.26.tar.bz2': '5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'}, + {'newlib-4.3.0.20230120.tar.gz': '83a62a99af59e38eb9b0c58ed092ee24d700fff43a22c03e433955113ef35150'}, + {'nvptx-tools-20230122.tar.gz': 'af05fac26e9a83d337758a5495dc35f7a7bbfd90cd09f4a5d3242d059f235e08'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, +] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.40'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +# Perl is only required when building with NVPTX support +if withnvptx: + osdependencies = ['perl'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb new file mode 100644 index 000000000000..5805f7d8a961 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb @@ -0,0 +1,63 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '13.1.0' + +homepage = 'https://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = SYSTEM + +source_urls = [ + 'https://ftpmirror.gnu.org/gnu/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'https://sourceware.org/pub/gcc/releases/gcc-%(version)s', # fallback URL for GCC + 'https://ftpmirror.gnu.org/gnu/gmp', # idem for GMP + 'https://ftpmirror.gnu.org/gnu/mpfr', # idem for MPFR + 'https://ftpmirror.gnu.org/gnu/mpc', # idem for MPC + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies + 'https://libisl.sourceforge.io/', # fallback URL for isl + 'https://sourceware.org/pub/newlib/', # for newlib + 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools +] +sources = [ + 'gcc-%(version)s.tar.gz', + 'gmp-6.2.1.tar.bz2', + 'mpfr-4.2.0.tar.bz2', + 'mpc-1.3.1.tar.gz', + 'isl-0.26.tar.bz2', + 'newlib-4.3.0.20230120.tar.gz', + {'download_filename': '93e0090.tar.gz', 'filename': 'nvptx-tools-20230122.tar.gz'}, +] +patches = [ + 'GCCcore-6.2.0-fix-find-isl.patch', + 'GCCcore-9.3.0_gmp-c99.patch', +] +checksums = [ + {'gcc-13.1.0.tar.gz': 'bacd4c614d8bd5983404585e53478d467a254249e0f1bb747c8bc6d787bd4fa2'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.2.0.tar.bz2': '691db39178e36fc460c046591e4b0f2a52c8f2b3ee6d750cc2eab25f1eaa999d'}, + {'mpc-1.3.1.tar.gz': 'ab642492f5cf882b74aa0cb730cd410a81edcdbec895183ce930e706c1c759b8'}, + {'isl-0.26.tar.bz2': '5eac8664e9d67be6bd0bee5085d6840b8baf738c06814df47eaf4166d9776436'}, + {'newlib-4.3.0.20230120.tar.gz': '83a62a99af59e38eb9b0c58ed092ee24d700fff43a22c03e433955113ef35150'}, + {'nvptx-tools-20230122.tar.gz': 'af05fac26e9a83d337758a5495dc35f7a7bbfd90cd09f4a5d3242d059f235e08'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, +] + +builddependencies = [ + ('M4', '1.4.19'), + ('binutils', '2.40'), +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True +withnvptx = True + +# Perl is only required when building with NVPTX support +if withnvptx: + osdependencies = ['perl'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb index 6cf3d77cc5c3..6babf890be57 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb @@ -43,6 +43,7 @@ dependencies = [ ('SciPy-bundle', '2022.05'), ('HDF5', '1.12.2'), ('HDF', '4.2.15'), + ('OpenJPEG', '2.5.0'), ] preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb index 01346b45e3a7..7e3c17c850fd 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb @@ -56,6 +56,7 @@ dependencies = [ ('Brunsli', '0.1'), ('Qhull', '2020.2'), ('LERC', '4.0.0'), + ('OpenJPEG', '2.5.0'), ] # common configopts for static, shared library builds diff --git a/easybuild/easyconfigs/g/GDCM/GDCM-3.0.21-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.21-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..298041d52e0e --- /dev/null +++ b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.21-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'GDCM' +version = '3.0.21' + +homepage = 'https://sourceforge.net/projects/gdcm' +description = "Grassroots DICOM: Cross-platform DICOM implementation" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['f29dbdd3b6b4c30c9803e6466b88b139d67f5585768565fe29f0be65ad737744'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +configopts = "-DGDCM_BUILD_DOCBOOK_MANPAGES=0" + +sanity_check_paths = { + 'files': ['lib/libgdcmCommon.a', 'lib/libgdcmDICT.a'], + 'dirs': ['include/gdcm-%(version_major_minor)s', 'lib/gdcm-%(version_major_minor)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..46eedfaa2dfd --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.4.2' + +homepage = 'https://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] +checksums = ['8d1c00c1018f96b4b97655482e57dcb0ce42ae2f1d349cd6d4191e7848d9ffe9'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.38'), +] + +dependencies = [ + ('X11', '20220504'), + ('Mesa', '22.0.3'), + ('libGLU', '9.0.2'), + ('freeglut', '3.2.2'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..6bd5ffab3985 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.4.2' + +homepage = 'https://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] +checksums = ['8d1c00c1018f96b4b97655482e57dcb0ce42ae2f1d349cd6d4191e7848d9ffe9'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +dependencies = [ + ('X11', '20221110'), + ('Mesa', '22.2.4'), + ('libGLU', '9.0.2'), + ('freeglut', '3.4.0'), + ('libpng', '1.6.38'), + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..ca2a334a1af7 --- /dev/null +++ b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-10.2.0.eb @@ -0,0 +1,53 @@ +easyblock = "ConfigureMake" + +name = "GLI" +version = "4.5.31" + +homepage = "https://pgi-jcns.fz-juelich.de/portal/pages/gli.html" +description = "Graphics Language Interpreter" + +toolchain = {"name": "GCCcore", "version": "10.2.0"} +toolchainopts = {"pic": True} + +source_urls = ["http://iffwww.iff.kfa-juelich.de/gli/"] +sources = [SOURCELOWER_TAR_GZ] +checksums = ["13b7def217672ab4fa01e39977af26f3fbbe0f7bbe7e7c42c2c4aa0ea5fc8c05"] + +builddependencies = [("binutils", "2.35")] + +dependencies = [ + ('X11', '20201008'), + ('zlib', '1.2.11'), + ('Tk', '8.6.10'), + ('Tcl', '8.6.10'), + ('libtirpc', '1.3.1') +] + +preconfigopts = 'cd src && ' +preconfigopts += 'sed -i -e "/ac_cv_c_zlib=.*with_zlib/s,},}/libz.so," configure && ' +configopts = 'CFLAGS=-DUSE_INTERP_RESULT LIBS=-ltirpc ' +configopts += '--with-zlib=$EBROOTZLIB/lib --with-zlibinclude=$EBROOTZLIB/include ' +configopts += '--with-tcllib=$EBROOTTCL/lib --with-tklib=$EBROOTTK/lib' + +prebuildopts = 'cd src &&' + +preinstallopts = 'cd src &&' + +parallel = 1 + +modextravars = { + "GLI_WSTYPE": "217", + "GLI_HOME": "%(installdir)s" +} + +modextrapaths = { + "PATH": "", + "LD_LIBRARY_PATH": "", +} + +sanity_check_paths = { + "files": ["libgks.a", "libgks.%s" % SHLIB_EXT, "libgli.a", "libgus.%s" % SHLIB_EXT], + "dirs": ["demo", "tcl/lib"], +} + +moduleclass = "vis" diff --git a/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..5f8d5037d42f --- /dev/null +++ b/easybuild/easyconfigs/g/GLI/GLI-4.5.31-GCCcore-12.2.0.eb @@ -0,0 +1,53 @@ +easyblock = "ConfigureMake" + +name = "GLI" +version = "4.5.31" + +homepage = "https://pgi-jcns.fz-juelich.de/portal/pages/gli.html" +description = "Graphics Language Interpreter" + +toolchain = {"name": "GCCcore", "version": "12.2.0"} +toolchainopts = {"pic": True} + +source_urls = ["http://iffwww.iff.kfa-juelich.de/gli/"] +sources = [SOURCELOWER_TAR_GZ] +checksums = ["13b7def217672ab4fa01e39977af26f3fbbe0f7bbe7e7c42c2c4aa0ea5fc8c05"] + +builddependencies = [("binutils", "2.39")] + +dependencies = [ + ('X11', '20221110'), + ('zlib', '1.2.12'), + ('Tk', '8.6.12'), + ('Tcl', '8.6.12'), + ('libtirpc', '1.3.3') +] + +preconfigopts = 'cd src && ' +preconfigopts += 'sed -i -e "/ac_cv_c_zlib=.*with_zlib/s,},}/libz.so," configure && ' +configopts = 'CFLAGS=-DUSE_INTERP_RESULT LIBS=-ltirpc ' +configopts += '--with-zlib=$EBROOTZLIB/lib --with-zlibinclude=$EBROOTZLIB/include ' +configopts += '--with-tcllib=$EBROOTTCL/lib --with-tklib=$EBROOTTK/lib' + +prebuildopts = 'cd src &&' + +preinstallopts = 'cd src &&' + +parallel = 1 + +modextravars = { + "GLI_WSTYPE": "217", + "GLI_HOME": "%(installdir)s" +} + +modextrapaths = { + "PATH": "", + "LD_LIBRARY_PATH": "", +} + +sanity_check_paths = { + "files": ["libgks.a", "libgks.%s" % SHLIB_EXT, "libgli.a", "libgus.%s" % SHLIB_EXT], + "dirs": ["demo", "tcl/lib"], +} + +moduleclass = "vis" diff --git a/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2021b.eb b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2021b.eb new file mode 100644 index 000000000000..0c453259ec8e --- /dev/null +++ b/easybuild/easyconfigs/g/GOATOOLS/GOATOOLS-1.3.1-foss-2021b.eb @@ -0,0 +1,58 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'PythonPackage' + +name = 'GOATOOLS' +version = '1.3.1' + +homepage = 'https://github.com/tanghaibao/goatools' +description = "A Python library for Gene Ontology analyses" + +toolchain = {'name': 'foss', 'version': '2021b'} + +# must download sources via git to preserve .git directory, +# since setuptools-scm is used to determine version +sources = [{ + 'git_config': { + 'url': 'https://github.com/tanghaibao', + 'repo_name': 'goatools', + 'tag': 'v%(version)s', + 'keep_git_dir': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [('cURL', '7.78.0')] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('XlsxWriter', '3.0.2'), + ('statsmodels', '0.13.1'), + ('pydot', '1.4.2'), + ('openpyxl', '3.0.9'), +] + +download_dep_fail = True +use_pip = True + +postinstallcmds = ["cp -a %(builddir)s/goatools/data/ %(installdir)s/"] + +sanity_check_paths = { + 'files': ['bin/find_enrichment.py'], + 'dirs': ['data', 'lib/python%(pyshortver)s/site-packages'], +} + +# example test run, see https://github.com/tanghaibao/goatools/blob/master/run.sh +sanity_check_commands = [ + "mkdir -p %(builddir)s", + "cd %(builddir)s && curl -OL http://geneontology.org/ontology/go-basic.obo", + "cd %(builddir)s && curl -OL http://www.geneontology.org/ontology/subsets/goslim_generic.obo", + "cd %(builddir)s && cp -a %(installdir)s/data .", + "cd %(builddir)s && find_enrichment.py --pval=0.05 --indent data/study data/population data/association", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3-GCC-11.3.0.eb new file mode 100644 index 000000000000..565232387de3 --- /dev/null +++ b/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3-GCC-11.3.0.eb @@ -0,0 +1,63 @@ +easyblock = 'Bundle' + +name = 'GOBNILP' +version = '1.6.3' +_nodots_version = version.replace('.', '') +_scip_version = '3.2.1' +_scip_nodots_version = _scip_version.replace('.', '') + +homepage = 'https://www.cs.york.ac.uk/aig/sw/gobnilp/' +description = """GOBNILP (Globally Optimal Bayesian Network learning using Integer Linear +Programming) is a C program which learns Bayesian networks from complete +discrete data or from local scores.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +dependencies = [ + ('SCIP', _scip_version), + ('ZIMPL', '3.3.4'), + ('SoPlex', '2.2.1'), + ('GMP', '6.2.1'), + ('libreadline', '8.1'), + ('ncurses', '6.3'), + ('zlib', '1.2.12'), +] + +default_easyblock = 'MakeCp' + +components = [ + ('LOP', _scip_version, { + 'source_urls': ['https://github.com/scipopt/scip/archive/refs/tags/'], + 'sources': ['v%s.tar.gz' % _scip_nodots_version], + 'patches': ['LOP-%(version)s_standalone-scip-lop-build.patch'], + 'checksums': [ + {'v321.tar.gz': + '015bdda4e681782fd03b61421b93aa3c1b913e5eea18bb8730d5fb9e4d67b4cb'}, + {'LOP-3.2.1_standalone-scip-lop-build.patch': + 'f996e56f1311fa4a613635b38969da731faf0ea9f10097799b1fa9a84598651e'}, + ], + 'start_dir': 'scip-%s/examples/%%(name)s' % _scip_nodots_version, + 'buildopts': '%(namelower)s COMP=gnu OPT=opt LPS=spx2', + 'files_to_copy': [(['bin/%(namelower)s'], 'bin')], + }), + (name, version, { + 'source_urls': ['http://www.cs.york.ac.uk/aig/sw/gobnilp'], + 'sources': ['%(namelower)s%(version)s.tar.gz'], + 'patches': ['%(name)s-%(version)s_use-eb-build-env.patch'], + 'checksums': [ + {'gobnilp1.6.3.tar.gz': + 'b31e5c87032f85f7404654beca47d472fd6c5dd7a5f82108bd5043ff0b8fa33c'}, + {'GOBNILP-1.6.3_use-eb-build-env.patch': + '9235ec8b9d05d9915f9961d4b46c2220e0d3b75f555a226a5667dcc69d76dae9'}, + ], + 'start_dir': '%(namelower)s' + _nodots_version, + 'files_to_copy': [(['bin/%(namelower)s'], 'bin')], + }), +] + +sanity_check_paths = { + 'files': ['bin/gobnilp', 'bin/lop'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3_use-eb-build-env.patch b/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3_use-eb-build-env.patch new file mode 100644 index 000000000000..e730aa76abfa --- /dev/null +++ b/easybuild/easyconfigs/g/GOBNILP/GOBNILP-1.6.3_use-eb-build-env.patch @@ -0,0 +1,79 @@ +Use build environment and dependencies from EasyBuild +author: Alex Domingo (Vrije Universiteit Brussel) +--- Makefile.orig 2023-03-31 18:33:07.943785000 +0200 ++++ Makefile 2023-03-31 18:42:53.636293000 +0200 +@@ -5,15 +5,25 @@ + # This file was created by editing the Makefile for the linear ordering + # example in SCIP + +-# Set the path the SCIP directory +-SCIPDIR = scip +- +-# Include default project Makefile from SCIP +-include $(SCIPDIR)/make/make.project ++# Set paths and flags to SCIP libraries ++SCIPDIR = $(EBROOTSCIP) ++SCIPLIB = scip ++OBJSCIPLIB = objscip ++LPILIB = lpispx2 ++NLPILIB = nlpi.cppad ++LPSLDFLAGS = -lzimpl -lsoplex -lgmp -lreadline -lncurses -lz ++ ++# Set paths to LOP ++LOPSRC = ../scip-321/examples/LOP/src ++LOPOBJ = ../scip-321/examples/LOP/obj/cons_linearordering.o + + # This missing for scip < 3 + VALGRIND = false + ++SRCDIR = src ++OBJDIR = obj ++BINDIR = bin ++ + # Declare the phony targets + .PHONY: all doxygen manual pedmanual gobnilp clean test + +@@ -46,7 +57,7 @@ + MAINSRC = $(wildcard $(SRCDIR)/*.c) + MAINOBJ = $(notdir $(MAINSRC:.c=.o)) + +-MAIN = $(MAINNAME).$(BASE).$(LPS)$(EXEEXTENSION) ++MAIN = $(MAINNAME) + MAINFILE = $(BINDIR)/$(MAIN) + ifeq ($(OSTYPE),mingw) + MAINSHORTLINK = $(BINDIR)/$(MAINNAME).exe +@@ -63,7 +74,7 @@ + LATEXCMD = @pdflatex -halt-on-error -interaction=errorstopmode + + #Needs to appear first so that "make" makes gobnilp +-gobnilp: $(SCIP) $(MAINFILE) $(MAINSHORTLINK) ++gobnilp: $(MAINFILE) $(MAINSHORTLINK) + + #----------------------------------------------------------------------- + #---------------------------- All ---------------------------- +@@ -161,19 +172,16 @@ + + $(MAINSHORTLINK): $(MAINFILE) + @rm -f $@ +- @cd $(dir $@) && ln -s $(notdir $(MAINFILE)) $(notdir $@) + +-$(MAINFILE): $(BINDIR) $(OBJDIR) $(SCIPLIBFILE) $(LPILIBFILE) $(NLPILIBFILE) $(MAINOBJFILES) +- @echo "-> linking $@" +- @$(LINKCXX) $(STATICFLAG) $(MAINOBJFILES) \ +- $(LINKCXX_L)$(SCIPDIR)/lib $(LINKCXX_l)$(SCIPLIB)$(LINKLIBSUFFIX) \ +- $(LINKCXX_l)$(OBJSCIPLIB)$(LINKLIBSUFFIX) $(LINKCXX_l)$(LPILIB)$(LINKLIBSUFFIX) $(LINKCXX_l)$(NLPILIB)$(LINKLIBSUFFIX) \ +- $(OFLAGS) $(LPSLDFLAGS) \ +- $(LDFLAGS) $(LINKCXX_o)$@ ++$(MAINFILE): $(BINDIR) $(OBJDIR) $(MAINOBJFILES) ++ echo "-> linking $@" ++ $(CXX) -static $(MAINOBJFILES) $(LOPOBJ) \ ++ -L$(SCIPDIR)/lib -l$(SCIPLIB) -l$(OBJSCIPLIB) -l$(LPILIB) -l$(NLPILIB) \ ++ $(LDFLAGS) $(LPSLDFLAGS) -o $@ + + $(OBJDIR)/%.o: $(SRCDIR)/%.c + @echo "-> compiling $*.c" +- @$(CC) $(FLAGS) $(OFLAGS) $(BINOFLAGS) $(CFLAGS) -c -g $< $(CC_o)$@ ++ @$(CC) $(CFLAGS) $(CPPFLAGS) -I$(LOPSRC) -c -g $< -o $@ + + $(OBJDIR): + @-mkdir -p $(OBJDIR) diff --git a/easybuild/easyconfigs/g/GOBNILP/LOP-3.2.1_standalone-scip-lop-build.patch b/easybuild/easyconfigs/g/GOBNILP/LOP-3.2.1_standalone-scip-lop-build.patch new file mode 100644 index 000000000000..9fbb54ef086c --- /dev/null +++ b/easybuild/easyconfigs/g/GOBNILP/LOP-3.2.1_standalone-scip-lop-build.patch @@ -0,0 +1,41 @@ +Build LOP example standalone without triggering a full build of SCIP +author: Alex Domingo (Vrije Universiteit Brussel) +--- Makefile.orig 2023-03-31 18:52:55.793723000 +0200 ++++ Makefile 2023-03-31 18:54:59.590029000 +0200 +@@ -29,6 +29,7 @@ + #----------------------------------------------------------------------------- + + include $(SCIPDIR)/make/make.project ++OBJDIR = obj + + #----------------------------------------------------------------------------- + # Main Program +@@ -39,9 +40,9 @@ + MAINSRC = $(addprefix $(SRCDIR)/,$(MAINOBJ:.o=.c)) + MAINDEP = $(SRCDIR)/depend.cmain.$(OPT) + +-MAIN = $(MAINNAME).$(BASE).$(LPS)$(EXEEXTENSION) ++MAIN = $(MAINNAME) + MAINFILE = $(BINDIR)/$(MAIN) +-MAINSHORTLINK = $(BINDIR)/$(MAINNAME) ++MAINSHORTLINK = $(MAINNAME) + MAINOBJFILES = $(addprefix $(OBJDIR)/,$(MAINOBJ)) + + #----------------------------------------------------------------------------- +@@ -79,7 +80,6 @@ + + $(MAINSHORTLINK): $(MAINFILE) + @rm -f $@ +- cd $(dir $@) && ln -s $(notdir $(MAINFILE)) $(notdir $@) + + $(OBJDIR): + @-mkdir -p $(OBJDIR) +@@ -123,7 +123,7 @@ + + + # main target +-$(MAINFILE): $(BINDIR) $(OBJDIR) $(SCIPLIBFILE) $(LPILIBFILE) $(NLPILIBFILE) $(MAINOBJFILES) ++$(MAINFILE): $(BINDIR) $(OBJDIR) $(MAINOBJFILES) + @echo "-> linking $@" + ifeq ($(VERBOSE),true) + $(LINKCXX) $(MAINOBJFILES) \ diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch new file mode 100644 index 000000000000..f52f396627aa --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch @@ -0,0 +1,53 @@ +From 79eb7a47726f7e0f644d0b9bddf3840b227a2f73 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Jens=20J=C3=B8rgen=20Mortensen?= +Date: Wed, 21 Sep 2022 12:10:16 +0200 +Subject: [PATCH] Test too strict for EasyBuild intel/2020b toolchain + +--- + gpaw/test/gllb/test_variants.py | 12 ++++++------ + 1 file changed, 6 insertions(+), 6 deletions(-) + +diff --git a/gpaw/test/gllb/test_variants.py b/gpaw/test/gllb/test_variants.py +index 0b9ede0..8a51261 100644 +--- a/gpaw/test/gllb/test_variants.py ++++ b/gpaw/test/gllb/test_variants.py +@@ -1,8 +1,8 @@ +-import pytest + import numpy as np ++import pytest + from ase.build import bulk +-from gpaw.test import gen + from gpaw import GPAW ++from gpaw.test import gen + + + def run(xc): +@@ -19,7 +19,7 @@ def run(xc): + xc=xc, + convergence={'density': 1e-5}, + kpts={'size': (1, 1, 1), 'gamma': True}, +- txt='{}.out'.format(xc)) ++ txt=f'{xc}.out') + atoms.calc = calc + atoms.get_potential_energy() + eig_n = calc.get_eigenvalues(kpt=0) +@@ -35,7 +35,7 @@ def test_wrappers(xc, in_tmp_dir, add_cwd_to_setup_paths): + # Check values against regular xc + ref_eig_n = run({'GLLBLDA': 'LDA', 'GLLBPBE': 'PBE'}[xc]) + assert np.allclose(eig_n, ref_eig_n, rtol=0, atol=1e-8), \ +- "{} error = {}".format(xc, np.max(np.abs(eig_n - ref_eig_n))) ++ f'{xc} error = {np.max(np.abs(eig_n - ref_eig_n))}' + + + refs = {'GLLB': +@@ -70,5 +70,5 @@ refs = {'GLLB': + def test_eigenvalues(xc, in_tmp_dir, add_cwd_to_setup_paths): + eig_n = run(xc) + ref_eig_n = refs[xc] +- assert np.allclose(eig_n, ref_eig_n, rtol=0, atol=5e-6), \ +- "{} error = {}".format(xc, np.max(np.abs(eig_n - ref_eig_n))) ++ assert np.allclose(eig_n, ref_eig_n, rtol=0, atol=2e-5), \ ++ f'{xc} error = {np.max(np.abs(eig_n - ref_eig_n))}' +-- +1.8.3.1 + diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb index a5bf81c6abc3..2a7e04552e67 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-foss-2022a.eb @@ -16,12 +16,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), ('GPAW-22.8.0-Remove-MPI-compiler-hack.patch', 0), + ('GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch', 1), ] checksums = [ - '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c', # gpaw-22.8.0.tar.gz - # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', - '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e', # GPAW-22.8.0-Remove-MPI-compiler-hack.patch + {'gpaw-22.8.0.tar.gz': '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, + {'GPAW-22.8.0-Remove-MPI-compiler-hack.patch': '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e'}, + {'GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch': + '207d98ab3b390330f832a77edf5e436b9ec46610add6c0487acaa63b2aa489a1'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb index 126147e70d50..8055d042a4ca 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-22.8.0-intel-2022a.eb @@ -16,12 +16,15 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), ('GPAW-22.8.0-Remove-MPI-compiler-hack.patch', 0), + ('GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch', 1), ] checksums = [ - '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c', # gpaw-22.8.0.tar.gz - # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15', - '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e', # GPAW-22.8.0-Remove-MPI-compiler-hack.patch + {'gpaw-22.8.0.tar.gz': '311eae8cb046f720e77e2e955042758c6e66d37c1fcbaf5d35e2834294a4ed6c'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, + {'GPAW-22.8.0-Remove-MPI-compiler-hack.patch': '44ca47fefb1bd409bae7da0a2f35125571dc927dc98f7cbca948ce86d25aa77e'}, + {'GPAW-22.8.0-Test-too-strict-for-EasyBuild.patch': + '207d98ab3b390330f832a77edf5e436b9ec46610add6c0487acaa63b2aa489a1'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.2-GCC-11.3.0.eb new file mode 100644 index 000000000000..8e6de771d67d --- /dev/null +++ b/easybuild/easyconfigs/g/GapFiller/GapFiller-2.1.2-GCC-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GapFiller' +version = '2.1.2' + +homepage = 'https://sourceforge.net/projects/gapfiller' +description = """GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. + It can be used for both DNA and RNA and it has been tested on Illumina data.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'cstd': 'c++11', 'extra_cxxflags': '-fpermissive'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a4c5235b1ee17e277d08cc945dbfa05af084559e546a2b7f15c9c1b703f4b237'] + +dependencies = [ + ('Boost', '1.79.0'), + ('zlib', '1.2.12'), +] + +buildopts = 'bin_PROGRAMS=GapFiller ' +buildopts += 'GapFiller_CFLAGS="$CFLAGS $LDFLAGS -lz" GapFiller_CXXFLAGS="$CXXFLAGS $LDFLAGS -lz"' +installopts = 'bin_PROGRAMS=GapFiller ' + +postinstallcmds = ["cp -a README %(installdir)s"] + +sanity_check_paths = { + 'files': ['bin/GapFiller', 'README'], + 'dirs': [], +} + +sanity_check_commands = ["GapFiller --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GenMap/GenMap-1.3.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GenMap/GenMap-1.3.0-GCCcore-11.2.0.eb new file mode 100755 index 000000000000..2a1f332ae414 --- /dev/null +++ b/easybuild/easyconfigs/g/GenMap/GenMap-1.3.0-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'GenMap' +version = '1.3.0' + +homepage = 'https://github.com/cpockrandt/genmap' + +description = """GenMap - Fast and Exact Computation of Genome Mappability""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/cpockrandt/genmap/archive/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['d237b284bb26d000039078e7be81bbebae21ee65d614ce89bd47a45f99fafb64'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.21.1'), + ('Python', '3.9.6'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('SeqAn', '2.4.0'), +] + +configopts = "-DSeqAn_DIR=$EBROOTSEQAN/util/cmake" + +sanity_check_paths = { + 'files': ["bin/genmap"], + 'dirs': [], +} + +sanity_check_commands = ["genmap %s --help" % x for x in ["", "index", "map"]] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2022a.eb b/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2022a.eb new file mode 100644 index 000000000000..a57ae34779fe --- /dev/null +++ b/easybuild/easyconfigs/g/GimmeMotifs/GimmeMotifs-0.17.2-foss-2022a.eb @@ -0,0 +1,77 @@ +easyblock = 'PythonBundle' + +name = 'GimmeMotifs' +version = '0.17.2' + +homepage = 'https://github.com/vanheeringen-lab/gimmemotifs' +description = "Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('pybedtools', '0.9.0'), + ('Pysam', '0.19.1'), + ('scikit-learn', '1.1.2'), + ('Seaborn', '0.12.1'), + ('statsmodels', '0.13.1'), + ('tqdm', '4.64.0'), + ('genomepy', '0.15.0'), + ('qnorm', '0.8.1'), + ('Arrow', '8.0.0'), # provides pyarrow, required by feather-format + ('HTSeq', '2.0.2'), # required by biofluff + ('pyBigWig', '0.3.18'), # required by biofluff +] + +use_pip = True + +exts_list = [ + ('palettable', '3.3.0', { + 'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'], + }), + ('biofluff', '3.0.4', { + 'modulename': 'fluff', + 'checksums': ['ef7b0a54103a830f197f21aa3d1ade8bdcddf613b437ea38c95260bb45324d6b'], + }), + ('diskcache', '5.4.0', { + 'checksums': ['8879eb8c9b4a2509a5e633d2008634fb2b0b35c2b36192d89655dbde02419644'], + }), + ('feather-format', '0.4.1', { + 'modulename': 'feather', + 'checksums': ['45f67e3745d394d4f160ca6d636bbfd4f8b68d01199dc1649b6e487d3e878903'], + }), + ('iteround', '1.0.4', { + 'source_urls': ['https://github.com/cgdeboer/iteround/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['445e4f0c793ae558e4db3cdee7e23d77459b9c586e8021667aa60c14ba7ff45f'], + }), + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + ('loguru', '0.6.0', { + 'checksums': ['066bd06758d0a513e9836fd9c6b5a75bfb3fd36841f4b996bc60b547a309d41c'], + }), + ('xxhash', '3.2.0', { + 'checksums': ['1afd47af8955c5db730f630ad53ae798cf7fae0acb64cebb3cf94d35c47dd088'], + }), + ('xdg', '6.0.0', { + 'checksums': ['24278094f2d45e846d1eb28a2ebb92d7b67fc0cab5249ee3ce88c95f649a1c92'], + }), + ('gimmemotifs', version, { + 'preinstallopts': """sed -i '/"configparser"/d' setup.py && """, + 'checksums': ['fbf70997abce6a75451c10b96994f8dbc03152b01df5cf30bf4397c98a9b54d2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/gimme'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["gimme --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.31-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.31-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..84adb82aa2ee --- /dev/null +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.31-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'GitPython' +version = '3.1.31' + +homepage = 'https://gitpython.readthedocs.org' +description = """ GitPython is a python library used to interact with Git repositories """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('git', '2.38.1', '-nodocs'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('smmap', '5.0.0', { + 'checksums': ['c840e62059cd3be204b0c9c9f74be2c09d5648eddd4580d9314c3ecde0b30936'], + }), + ('gitdb', '4.0.10', { + 'checksums': ['6eb990b69df4e15bad899ea868dc46572c3f75339735663b81de79b06f17eb9a'], + }), + (name, version, { + 'modulename': 'git', + 'checksums': ['8ce3bcf69adfdf7c7d503e78fd3b1c492af782d58893b650adb2ac8912ddd573'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb new file mode 100644 index 000000000000..2abdf04dc938 --- /dev/null +++ b/easybuild/easyconfigs/g/GlimmerHMM/GlimmerHMM-3.0.4c-GCC-11.2.0.eb @@ -0,0 +1,57 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'GlimmerHMM' +version = '3.0.4c' + +homepage = 'https://ccb.jhu.edu/software/glimmerhmm' +description = """GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. + Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally + it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted + from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ccb.jhu.edu/software/%(namelower)s/dl'] +sources = [SOURCE_TAR_GZ] +checksums = ['31ee2ceb8f31338205b2de626d83d0f92d2cd55a04d48a6803193a2d0ad1b4a3'] + +dependencies = [ + ('Perl', '5.34.0'), +] + +start_dir = 'sources' + +# make sure -O0 is not used as compiler option +prebuildopts = "ls makefile train/makefile | xargs sed -i 's/-O0 .*//g' && " + +# also build in 'train' subdirectory to overwrite pre-compiled binaries +buildopts = "&& cd ../train && make" + +local_train_files = ['build1', 'build2', 'build-icm', 'build-icm-noframe', 'erfapp', 'falsecomp', + 'findsites', 'karlin', 'score', 'score2', 'scoreATG', 'scoreATG2', 'scoreSTOP', + 'scoreSTOP2', 'splicescore', 'trainGlimmerHMM'] +files_to_copy = [ + (['sources/%(namelower)s'], 'bin'), + (['train/%s' % x for x in local_train_files], 'bin'), + (['train/*.pm'], 'lib/perl%(perlmajver)s'), + 'trained_dir', 'README', 'train/readme.train', +] + +fix_perl_shebang_for = ['bin/trainGlimmerHMM'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['trained_dir'], +} + +sanity_check_commands = [ + "%(namelower)s -h", + r"trainGlimmerHMM -h 2>&1 | grep '^[ ]*Train GlimmerHMM module'", +] + +modextrapaths = {'PERL5LIB': 'lib/perl%(perlmajver)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb new file mode 100644 index 000000000000..e462c994af7f --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-iomkl-2021a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GlobalArrays' +version = '5.8' + +homepage = 'https://hpc.pnl.gov/globalarrays' +description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" + +toolchain = {'name': 'iomkl', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/%(name)s/ga/releases/download/'] +sources = ['v%(version)s/ga-%(version)s.tar.gz'] +checksums = ['64df7d1ea4053d24d84ca361e67a6f51c7b17ed7d626cb18a9fbc759f4a078ac'] + +configopts = ' --with-mpi --enable-i8 ' +configopts += '--with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64" ' +configopts += '--with-scalapack8="L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' +configopts += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' +# select armci network as (Comex) MPI-1 two-sided +configopts += ' --with-mpi-ts' + + +sanity_check_paths = { + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', + 'lib/libcomex.a', 'lib/libga.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/Go/Go-1.18.3.eb b/easybuild/easyconfigs/g/Go/Go-1.18.3.eb index cb532faf4801..fc45e80f1ebc 100644 --- a/easybuild/easyconfigs/g/Go/Go-1.18.3.eb +++ b/easybuild/easyconfigs/g/Go/Go-1.18.3.eb @@ -16,7 +16,10 @@ source_urls = ['https://storage.googleapis.com/golang/'] local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'} sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]] -checksums = ['956f8507b302ab0bb747613695cdae10af99bbd39a90cae522b7c0302cc27245'] +checksums = [{ + 'go%(version)s.linux-amd64.tar.gz': '956f8507b302ab0bb747613695cdae10af99bbd39a90cae522b7c0302cc27245', + 'go%(version)s.linux-arm64.tar.gz': 'beacbe1441bee4d7978b900136d1d6a71d150f0a9bb77e9d50c822065623a35a', +}] sanity_check_paths = { 'files': ['bin/go', 'bin/gofmt'], diff --git a/easybuild/easyconfigs/g/Go/Go-1.20.4.eb b/easybuild/easyconfigs/g/Go/Go-1.20.4.eb new file mode 100644 index 000000000000..a294c0de68fc --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.20.4.eb @@ -0,0 +1,34 @@ +# Update to 1.20.4 +# Jordi Camps / CNAG +# Sebastien Moretti / SIB + +easyblock = 'Tarball' + +name = 'Go' +version = "1.20.4" + +homepage = 'https://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = SYSTEM + +source_urls = ['https://storage.googleapis.com/golang/'] + +local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'} +sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]] +checksums = [{ + 'go%(version)s.linux-amd64.tar.gz': '698ef3243972a51ddb4028e4a1ac63dc6d60821bf18e59a807e051fee0a385bd', + 'go%(version)s.linux-arm64.tar.gz': '105889992ee4b1d40c7c108555222ca70ae43fccb42e20fbf1eebb822f5e72c6', +}] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +sanity_check_commands = ["go help"] + +modextravars = {'GOROOT': '%(installdir)s'} + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..cd161186dfc8 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-3.0.9-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '3.0.9' + +homepage = 'https://www.gnu.org/software/guile/' + +description = """ + Guile is a programming language, designed to help programmers create flexible + applications that can be extended by users or other programmers with plug-ins, + modules, or scripts. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['18525079ad29a0d46d15c76581b5d91c8702301bfd821666d2e1d13726162811'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('gc', '8.2.2'), + ('GMP', '6.2.0'), + ('libffi', '3.3'), + ('libunistring', '1.1'), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s guile guile%(version_major)s"] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', + 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', + 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', + 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..4eeb0dae6214 --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-10.0.1-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +name = 'Gurobi' +version = '10.0.1' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['%(namelower)s%(version)s_linux64.tar.gz'] +patches = ['%(name)s-9.0.1_use-eb-python-gurobi-shell.patch'] +checksums = [ + {'gurobi10.0.1_linux64.tar.gz': 'a0b551156df2c94107b3428cae278716a0a6c913f63ac132573852b9725b6c59'}, + {'Gurobi-9.0.1_use-eb-python-gurobi-shell.patch': + 'b4a998182d05f969d1de519f4746ac9e0c6646dd35233231b6ab5963dfa67d01'}, +] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python*'] + +# license is mandatory for installation +# use EB_GUROBI_LICENSE_FILE environment variable, or +# uncomment and modify the following variable: +# license_file = '/path/to/my-license-file' + +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..5061399f2ff5 --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-8.2.2-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '8.2.2' +local_libatomic_version = '7.8.0' + +homepage = 'https://hboehm.info/gc/' +description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a + garbage collecting replacement for C malloc or C++ new. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'https://github.com/ivmai/bdwgc/releases/download/v%(version)s/', # preferred for gc-%(version)s.tar.gz + 'https://hboehm.info/gc/gc_source/', # alternate for gc-%(version)s.tar.gz + 'https://github.com/ivmai/libatomic_ops/releases/download/v%s/' % local_libatomic_version, +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-%s.tar.gz' % local_libatomic_version, +] +checksums = [ + {'gc-8.2.2.tar.gz': 'f30107bcb062e0920a790ffffa56d9512348546859364c23a14be264b38836a0'}, + {'libatomic_ops-7.8.0.tar.gz': '15676e7674e11bda5a7e50a73f4d9e7d60452271b8acf6fd39a71fefdf89fa31'}, +] + +builddependencies = [ + ('binutils', '2.35'), +] + +preconfigopts = 'ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && ' + +configopts = "--enable-static" + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, + 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022b.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022b.eb new file mode 100644 index 000000000000..a887dfe6e148 --- /dev/null +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'geopandas' +version = '0.12.2' + +homepage = 'https://github.com/geopandas/geopandas' +description = """GeoPandas is a project to add support for geographic data to pandas objects. +It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series +and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and +perform geometric operations.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Shapely', '2.0.1'), + ('Fiona', '1.9.2'), + ('matplotlib', '3.7.0'), + ('pyproj', '3.5.0'), + ('networkx', '3.0'), # needed by mapclassify + ('scikit-learn', '1.2.1'), # needed by mapclassify +] + +use_pip = True + +exts_list = [ + ('mapclassify', '2.4.3', { + 'checksums': ['51b81e1f1ee7f64a4ca1e9f61f01216c364a3f086a48b1be38eb057199cb19bf'], + }), + (name, version, { + 'checksums': ['0acdacddefa176525e4da6d9aeeece225da26055c4becdc6e97cf40fa97c27f4'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..d3c0439ba9c6 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.21.1' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e8c3650e1d8cee875c4f355642382c1df83058bd5a11ee8555c0cf276d646d45'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('libxml2', '2.11.4'), + ('ncurses', '6.4'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..d54ca5d04538 --- /dev/null +++ b/easybuild/easyconfigs/g/googletest/googletest-1.13.0-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'googletest' +version = '1.13.0' + +homepage = 'https://github.com/google/googletest' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/google/googletest/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ad7fdba11ea011c1d925b3289cf4af2c66a352e18d4c7264392fead75e919363'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] +# build twice, once for static, once for shared libraries +configopts = ['', ' -DBUILD_SHARED_LIBS=ON '] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (local_lib, local_ext) for local_lib in ['gmock', 'gmock_main', 'gtest', 'gtest_main'] + for local_ext in ['a', SHLIB_EXT]], + 'dirs': ['include/gmock', 'include/gtest'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gpustat/gpustat-1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/gpustat/gpustat-1.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..a581373ba1e6 --- /dev/null +++ b/easybuild/easyconfigs/g/gpustat/gpustat-1.1-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'gpustat' +version = '1.1' + +homepage = 'https://github.com/wookayin/gpustat' +description = "A simple command-line utility for querying and monitoring GPU status" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +# This software works directly against the nvidia drivers and doesn't require CUDA. +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +exts_list = [ + ('blessed', '1.20.0', { + 'checksums': ['2cdd67f8746e048f00df47a2880f4d6acbcdb399031b604e34ba8f71d5787680'], + }), + ('nvidia-ml-py', '11.525.112', { + 'modulename': 'pynvml', + 'checksums': ['c64e473953b65ec0ccc76cf3601c3130a0ac8060bbcaea912cc00fa8e4c9868d'], + }), + (name, version, { + 'checksums': ['c8fc105404aac11884f70ed2fa06cfd210d3cd389ccae4a9bc38579c72460cee'], + }), +] + +sanity_check_paths = { + 'files': ['bin/gpustat'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["gpustat --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..0c6ebe10a4c3 --- /dev/null +++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'graphite2' +version = '1.3.14' + +homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home' +description = """Graphite is a "smart font" system developed specifically to + handle the complexities of lesser-known languages of the world.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/silnrsi/graphite/archive/'] +sources = ['%(version)s.zip'] +checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['bin/gr2fonttest'] + + ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']], + 'dirs': ['include/%(name)s', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..957f3fbd53c1 --- /dev/null +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'groff' +version = '1.22.4' + +homepage = 'https://www.gnu.org/software/groff' +description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands + and produces formatted output.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.gnu.org/gnu/groff'] +sources = [SOURCE_TAR_GZ] +checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] + +builddependencies = [ + ('binutils', '2.40'), +] + +configopts = '--with-doc=no' + +sanity_check_paths = { + 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], + 'dirs': ['lib/groff', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..917a74687949 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'gzip' +version = '1.12' + +homepage = 'https://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['gzip-1.12_fix-gnulib-strndup-redeclaration.patch'] +checksums = [ + '5b4fb14d38314e09f2fc8a1c510e7cd540a3ea0e3eb9b0420046b82c3bf41085', # gzip-1.12.tar.gz + # gzip-1.12_fix-gnulib-strndup-redeclaration.patch + '9c67e3e88848f7ff1f19f29d87f286bac1cc8f027f7eea9bcaf53883b95032e4', +] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 000000000000..0b7aef323431 --- /dev/null +++ b/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'HD-BET' +version = '20220318' +versionsuffix = '-CUDA-%(cudaver)s' +_commit = '56c7fb8e6509563aa6377cdb0f2dd4e7ad359252' + +homepage = 'https://github.com/MIC-DKFZ/HD-BET' +description = "Tool for brain extraction." + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'MIC-DKFZ' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%s.tar.gz' % _commit] +checksums = ['744eb7b084feefb4243855529537a47fa4d1c1d93b6b967969c2ede8b9b8b46a'] + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('PyTorch', '1.10.0', versionsuffix), + ('scikit-image', '0.18.3'), + ('SimpleITK', '2.1.1'), + ('batchgenerators', '0.25'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'HD_BET'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a.eb b/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a.eb new file mode 100644 index 000000000000..e671387837ef --- /dev/null +++ b/easybuild/easyconfigs/h/HD-BET/HD-BET-20220318-foss-2021a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'HD-BET' +version = '20220318' +_commit = '56c7fb8e6509563aa6377cdb0f2dd4e7ad359252' + +homepage = 'https://github.com/MIC-DKFZ/HD-BET' +description = "Tool for brain extraction." + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'MIC-DKFZ' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%s.tar.gz' % _commit] +checksums = ['744eb7b084feefb4243855529537a47fa4d1c1d93b6b967969c2ede8b9b8b46a'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('PyTorch', '1.10.0'), + ('scikit-image', '0.18.3'), + ('SimpleITK', '2.1.1'), + ('batchgenerators', '0.25'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'HD_BET'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb new file mode 100644 index 000000000000..ddde88aa0685 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.6-iompi-2020a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.6' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iompi', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb new file mode 100644 index 000000000000..2b0187340e21 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.7-iompi-2021a.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.10.7' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iompi', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15'] +dependencies = [ + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), +] + + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2022a.eb b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2022a.eb new file mode 100644 index 000000000000..1e8dd76e7080 --- /dev/null +++ b/easybuild/easyconfigs/h/HH-suite/HH-suite-3.3.0-gompi-2022a.eb @@ -0,0 +1,90 @@ +## +# This file is an EasyBuild recipy as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# Updated to use gompi-2020b toolchain: +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'HH-suite' +version = '3.3.0' + +homepage = 'https://github.com/soedinglab/hh-suite' +description = """The HH-suite is an open-source software package + for sensitive protein sequence searching based on the pairwise + alignment of hidden Markov models (HMMs).""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/soedinglab/hh-suite/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dd67f7f3bf601e48c9c0bc4cf1fbe3b946f787a808bde765e9436a48d27b0964'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Perl', '5.34.1'), + ('Python', '3.10.4'), +] + +_binaries_help = [ + 'cstranslate', 'cstranslate_mpi', 'hhalign', 'hhalign_mpi', 'hhalign_omp', 'hhconsensus', + 'hhfilter', 'hhmake' +] + +_binaries_h = [ + 'a3m_database_extract', 'a3m_database_filter', 'a3m_database_reduce', 'a3m_extract', 'a3m_reduce', + 'hhblits', 'hhblits_ca3m', 'hhblits_mpi', 'hhblits_omp', 'hhsearch', 'hhsearch_mpi', 'hhsearch_omp' +] + +_binaries_version = ['ffindex_build', 'ffindex_from_fasta', 'ffindex_modify'] + +_binaries_v = ['ffindex_from_fasta_with_split'] + +_binaries_helpless = [ + 'ffindex_apply', 'ffindex_apply_mpi', 'ffindex_get', + 'ffindex_order', 'ffindex_reduce', 'ffindex_unpack' +] + +_scriptfiles = ['hhmakemodel.py', 'hh_reader.py', 'hhsuitedb.py', 'cif2fasta.py'] + +fix_perl_shebang_for = ['scripts/*pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries_help] + + ['bin/%s' % x for x in _binaries_h] + + ['bin/%s' % x for x in _binaries_version] + + ['bin/%s' % x for x in _binaries_v] + + ['bin/%s' % x for x in _binaries_helpless] + + ['scripts/%s' % y for y in _scriptfiles], + 'dirs': ['data', 'scripts'] +} + +sanity_check_commands = ['%s --help' % x for x in _binaries_help] +sanity_check_commands += ['%s -h' % x for x in _binaries_h] +sanity_check_commands += ['%s --version' % x for x in _binaries_version] +sanity_check_commands += ['%s -v' % x for x in _binaries_v] +sanity_check_commands += ['%s 2>&1 | grep USAGE' % x for x in _binaries_helpless] + +modextrapaths = { + 'PATH': 'scripts', + 'PERL5LIB': 'scripts', +} + +modextravars = { + 'HHLIB': '%(installdir)s', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023.03.eb new file mode 100644 index 000000000000..10fe0118177e --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2023.03.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2023.03'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb new file mode 100644 index 000000000000..e9af6f663733 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-0.15-foss-2022a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'HTSplotter' +version = '0.15' + +homepage = 'https://github.com/CBIGR/HTSplotter' +description = """HTSplotter allows an end-to-end data processing and analysis of chemical and genetic in vitro +perturbation screens.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('h5py', '3.7.0'), + ('Seaborn', '0.12.1'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('minio', '7.1.13', { + 'checksums': ['8828615a20cde82df79c5a52005252ad29bb022cde25177a4a43952a04c3222c'], + }), + ('pypdf', '3.4.1', { + 'checksums': ['8b0badc787062e8fb0d8393eb2a76903717fb24e5cc84e2b03cde5ac3881700f'], + }), + ('PyPDF2', '3.0.1', { + 'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'], + 'modulename': 'PyPDF2', + }), + ('PyPDF3', '1.0.6', { + 'checksums': ['c946f3273419e37258e35e72273f49904ab15723d87a761c1115ef99799f8c5f'], + 'modulename': 'PyPDF3', + }), + (name, version, { + 'checksums': ['9504709ac2d04dbcd0694ca0370a44b7e302b667771fb492b596d9662a2a85a9'], + 'modulename': 'HTSplotter', + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2022b.eb b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2022b.eb new file mode 100644 index 000000000000..00810cd3b194 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2022b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'HTSplotter' +version = '2.11' + +homepage = 'https://github.com/CBIGR/HTSplotter' +description = """HTSplotter allows an end-to-end data processing and analysis of chemical and genetic in vitro +perturbation screens.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('matplotlib', '3.7.0'), + ('h5py', '3.8.0'), + ('Seaborn', '0.12.2'), + ('tqdm', '4.64.1'), +] + +use_pip = True + +exts_list = [ + ('minio', '7.1.13', { + 'checksums': ['8828615a20cde82df79c5a52005252ad29bb022cde25177a4a43952a04c3222c'], + }), + ('pypdf', '3.6.0', { + 'checksums': ['7d7bd0603f4e87a7064597aa968fcf77a065b596cfbe6e5003a5b00a043db230'], + }), + ('PyPDF2', '3.0.1', { + 'modulename': 'PyPDF2', + 'checksums': ['a74408f69ba6271f71b9352ef4ed03dc53a31aa404d29b5d31f53bfecfee1440'], + }), + ('PyPDF3', '1.0.6', { + 'modulename': 'PyPDF3', + 'checksums': ['c946f3273419e37258e35e72273f49904ab15723d87a761c1115ef99799f8c5f'], + }), + (name, version, { + 'modulename': 'HTSplotter', + 'checksums': ['51c0cee4e8eeecfd03f32dd707e0fa433cec91abb9334ec1d28e7f82615dbe29'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4.2-foss-2020b.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4.2-foss-2020b.eb new file mode 100644 index 000000000000..7065f827a27e --- /dev/null +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4.2-foss-2020b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Harminv' +version = '1.4.2' + +homepage = 'https://github.com/stevengj/harminv' +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - + given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially + decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those + sinusoids.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'cstd': 'c99'} + +source_urls = ['https://github.com/stevengj/harminv/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5a9a1bf710972442f065d0d62c62d0c4ec3da4a3696d7160a35602c9470bc7a2'] + +builddependencies = [('pkg-config', '0.29.2')] + +configopts = "--with-pic --with-blas=openblas --with-lapack=openblas --enable-shared" + +sanity_check_paths = { + 'files': ['bin/harminv', 'lib/libharminv.a', 'lib/libharminv.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..a05239847d3c --- /dev/null +++ b/easybuild/easyconfigs/h/Highway/Highway-1.0.4-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'Highway' +version = '1.0.4' + +homepage = 'https://github.com/google/highway' + +description = """Highway is a C++ library for SIMD (Single Instruction, Multiple Data), i.e. applying the same +operation to 'lanes'.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/google/highway/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['faccd343935c9e98afd1016e9d20e0b8b89d908508d1af958496f8c2d3004ac2'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('googletest', '1.13.0'), +] + +configopts = "-DHWY_SYSTEM_GTEST=ON" + +runtest = "test" + +sanity_check_paths = { + 'files': ['lib/libhwy.a'], + 'dirs': ['include/hwy'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-intel-2021a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-intel-2021a.eb new file mode 100644 index 000000000000..900b8bfcad7d --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.21.0-intel-2021a.eb @@ -0,0 +1,21 @@ +## +# Author: Robert Mijakovic +## +name = 'Hypre' +version = '2.21.0' + +homepage = 'https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods' +description = """Hypre is a library for solving large, sparse linear systems of equations on massively + parallel computers. The problems of interest arise in the simulation codes being developed at LLNL + and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/hypre-space/hypre/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e380f914fe7efe22afc44cdf553255410dc8a02a15b2e5ebd279ba88817feaf5'] + +start_dir = 'src' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.1.0-foss-2021b.eb b/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.1.0-foss-2021b.eb new file mode 100644 index 000000000000..7efee9efd0aa --- /dev/null +++ b/easybuild/easyconfigs/h/h5netcdf/h5netcdf-1.1.0-foss-2021b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'h5netcdf' +version = '1.1.0' + +homepage = 'https://h5netcdf.org/' +description = """A Python interface for the netCDF4 file-format that reads and writes local or +remote HDF5 files directly via h5py or h5pyd, without relying on the Unidata +netCDF library.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('h5py', '3.6.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['932c3b573bed7370ebfc9e802cd60f1a4da5236efb11b36eeff897324d76bf56'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..d3579d82fd85 --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.49.3' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['4d7e4fdef2eca6afe07a2682151cea78781e0a4e8f9622142d9f70c083a2fd4f'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.40', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.1.0.eb b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..7cf3afc6f6cc --- /dev/null +++ b/easybuild/easyconfigs/h/help2man/help2man-1.49.3-GCCcore-13.1.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'help2man' +version = '1.49.3' + +homepage = 'https://www.gnu.org/software/help2man/' +description = """help2man produces simple manual pages from the '--help' and '--version' output of other commands.""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['4d7e4fdef2eca6afe07a2682151cea78781e0a4e8f9622142d9f70c083a2fd4f'] + +builddependencies = [ + # use same binutils version that was used when building GCC toolchain + ('binutils', '2.40', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/help2man'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb index 57bf257cf0c7..138f1ab5d112 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb @@ -24,6 +24,10 @@ dependencies = [ use_pip = True +# WARNING: the versions of ipywidgets, widgetsnbextension and jupyterlab_widgets are tied between them +# use the versions published in a single release commit instead of blindly pushing to last available version, +# see for instance https://github.com/jupyter-widgets/ipywidgets/commit/c5fac25d17a93faf7bea66f5d103c605a9f19ddb + exts_list = [ ('ipython_genutils', '0.2.0', { 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], @@ -38,8 +42,9 @@ exts_list = [ ('prompt_toolkit', '3.0.31', { 'checksums': ['9ada952c9d1787f52ff6d5f3484d0b4df8952787c087edf6a1f7c2cb1ea88148'], }), - ('traitlets', '5.2.0', { - 'checksums': ['60474f39bf1d39a11e0233090b99af3acee93bbc2281777e61dd8c87da8a0014'], + ('traitlets', '5.2.1.post0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['f44b708d33d98b0addb40c29d148a761f44af740603a8fd0e2f8b5b27cf0f087'], }), ('parso', '0.8.3', { 'checksums': ['8c07be290bb59f03588915921e29e8a50002acaf2cdc5fa0e0114f91709fafa0'], @@ -126,8 +131,8 @@ exts_list = [ ('prometheus_client', '0.11.0', { 'checksums': ['3a8baade6cb80bcfe43297e33e7623f3118d660d41387593758e2fb1ea173a86'], }), - ('ipywidgets', '7.6.3', { - 'checksums': ['9f1a43e620530f9e570e4a493677d25f08310118d315b00e25a18f12913c41f0'], + ('ipywidgets', '7.7.4', { + 'checksums': ['e2cca1f95b4b8e96e5c2c6ac7cfebacafb924a473df94a243a5e68b7b23172c7'], }), ('deprecation', '2.1.0', { 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], @@ -138,8 +143,8 @@ exts_list = [ ('jupyterlab_pygments', '0.1.2', { 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], }), - ('jupyterlab_widgets', '3.0.3', { - 'checksums': ['c767181399b4ca8b647befe2d913b1260f51bf9d8ef9b7a14632d4c1a7b536bd'], + ('jupyterlab_widgets', '1.1.3', { + 'checksums': ['5285a4316e13f9a6512cb80a0cfec5aafa2c336097ae077a07a60c145f2154fc'], }), ('argon2-cffi', '20.1.0', { 'modulename': 'argon2', @@ -148,8 +153,8 @@ exts_list = [ ('notebook', '6.4.0', { 'checksums': ['9c4625e2a2aa49d6eae4ce20cbc3d8976db19267e32d2a304880e0c10bf8aef9'], }), - ('widgetsnbextension', '3.5.1', { - 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + ('widgetsnbextension', '3.6.3', { + 'checksums': ['28cb103f3066a6fdd6fd63264dd2a9709266c351a9a5c4a50a0bfd5ae2557b46'], }), ('matplotlib-inline', '0.1.2', { 'checksums': ['f41d5ff73c9f5385775d5c0bc13b424535c8402fe70ea8210f93e11f3683993e'], diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.3-gompi-2022a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.3-gompi-2022a.eb new file mode 100644 index 000000000000..0ea0821beb2f --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.3-gompi-2022a.eb @@ -0,0 +1,57 @@ +# Updated to v2.1.3 by +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'IQ-TREE' +version = '2.2.2.3' + +# HTTPS is not working +homepage = 'http://www.iqtree.org/' +description = """Efficient phylogenomic software by maximum likelihood""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary + +source_urls = ['https://github.com/iqtree/iqtree2/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'IQ-TREE-2.1.2_use_EB_LSD2.patch', + 'IQ-TREE-2.2.1_fix-mpi.patch', +] +checksums = [ + {'v2.2.2.3.tar.gz': 'fb15dfcdf63ce20f371763fff925804809f2fd5b7faaad1fb09a6f2bc7c2ba01'}, + {'IQ-TREE-2.1.2_use_EB_LSD2.patch': 'daa2ab12d44e26eb5607c4ed6acb9d970e230a83dabcf21461f37bc48263b816'}, + {'IQ-TREE-2.2.1_fix-mpi.patch': '9ead6808efd11d4c01dd265cca6094cffd6377746d3b2fc84b43d2faeee0777c'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Eigen', '3.4.0'), +] +dependencies = [ + ('zlib', '1.2.12'), + ('Boost', '1.79.0'), + ('LSD2', '2.3'), +] + +local_conf_opts = ' -DUSE_LSD2=ON ' +configopts = [ + '-DIQTREE_FLAGS=omp' + local_conf_opts, + '-DIQTREE_FLAGS=mpi -DCMAKE_C_COMPILER="$MPICC" -DCMAKE_CXX_COMPILER="$MPICXX"' + local_conf_opts, +] + +sanity_check_paths = { + 'files': ['bin/iqtree2', 'bin/iqtree2-mpi'], + 'dirs': [], +} + +sanity_check_commands = [ + "iqtree2 --help", + "mkdir -p $TMPDIR/{test-omp,test-mpi}", + "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy", + "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/ITSx/ITSx-1.1.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/ITSx/ITSx-1.1.3-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..7392f5fd08ae --- /dev/null +++ b/easybuild/easyconfigs/i/ITSx/ITSx-1.1.3-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'ITSx' +version = '1.1.3' + +homepage = 'https://microbiology.se/software/itsx/' +description = '''ITSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of +fungi and other eukaryotes for use in environmental sequencing.''' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://microbiology.se/sw/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['6f6d7ff6350f82439dee5348f6e8bda512be25193c603d4e56cc215c520091bf'] + +dependencies = [('Perl', '5.34.1')] + +fix_perl_shebang_for = ['ITSx'] + +sanity_check_paths = { + 'files': ['ITSx'], + 'dirs': ['ITSx_db'], +} + +sanity_check_commands = ['ITSx --help'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IgBLAST/IgBLAST-1.21.0-x64-linux.eb b/easybuild/easyconfigs/i/IgBLAST/IgBLAST-1.21.0-x64-linux.eb new file mode 100644 index 000000000000..8d3bf7d2572c --- /dev/null +++ b/easybuild/easyconfigs/i/IgBLAST/IgBLAST-1.21.0-x64-linux.eb @@ -0,0 +1,30 @@ +# Easybuild Easyconfig +# +# John Dey +# +# Fred Hutchinson Cancer Center - Seattle Washington +easyblock = "Tarball" + +name = 'IgBLAST' +version = '1.21.0' +versionsuffix = '-x64-linux' + +homepage = 'https://ncbi.github.io/igblast' +description = """IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.""" + +toolchain = SYSTEM + +source_urls = ['ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/%(version)s'] +sources = ['ncbi-%(namelower)s-%(version)s-x64-linux.tar.gz'] +checksums = ['737d19aed8f3d8d717fcd8a2fa22e93b0830dd9cced729f41a67df95c8aef136'] + +sanity_check_paths = { + 'files': ["bin/igblastn", 'bin/igblastp'], + 'dirs': ['bin'] +} + +sanity_check_commands = ['%(namelower)sn -h'] + +modextravars = {'IGDATA': '%(installdir)s/internal_data'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/Imath/Imath-3.1.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/Imath/Imath-3.1.7-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..b6497fabaebf --- /dev/null +++ b/easybuild/easyconfigs/i/Imath/Imath-3.1.7-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Imath' +version = '3.1.7' + +homepage = 'https://imath.readthedocs.io/en/latest/' +description = """ +Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/AcademySoftwareFoundation/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['bff1fa140f4af0e7f02c6cb78d41b9a7d5508e6bcdfda3a583e35460eb6d4b47'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['lib/libImath.%s' % SHLIB_EXT], + 'dirs': ['include/Imath'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb new file mode 100644 index 000000000000..57d29e7b2b7c --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2022b.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# Updated:: Denis Kristak (INUITS) +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'Infernal' +version = "1.1.4" + +homepage = 'http://eddylab.org/infernal/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = ['http://eddylab.org/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc'] + +local_bins = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat'] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in local_bins], + 'dirs': [] +} + +sanity_check_commands = ['cm%s -h' % x for x in local_bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb index d45355114798..aa12f6d8bf51 100644 --- a/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb +++ b/easybuild/easyconfigs/i/InterProScan/InterProScan-5.55-88.0-foss-2021a.eb @@ -27,6 +27,7 @@ dependencies = [ ('Perl', '5.32.1'), ('libgd', '2.3.1'), ('Python', '3.9.5'), + ('PCRE', '8.44'), ] # NOTE some analyses done by InterProScan require extra tools not included in the interproscan # distribution because of license issues. diff --git a/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb new file mode 100644 index 000000000000..5e8f0c47b88e --- /dev/null +++ b/easybuild/easyconfigs/i/IsoSeq/IsoSeq-3.8.2-linux-x86_64.eb @@ -0,0 +1,40 @@ +easyblock = "Binary" + +name = "IsoSeq" +version = "3.8.2" +versionsuffix = "-linux-x86_64" + +homepage = "https://github.com/PacificBiosciences/ioseq3" +description = """IsoSeq v3 contains the newest tools to identify transcripts + in PacBio single-molecule sequencing data. Starting in SMRT + Link v6.0.0, those tools power the IsoSeq GUI-based analysis + application. A composable workflow of existing tools and + algorithms, combined with a new clustering technique, allows + to process the ever-increasing yield of PacBio machines with + similar performance to IsoSeq versions 1 and 2. Starting with + version 3.4, support for UMI and cell barcode based + deduplication has been added. + """ + +toolchain = SYSTEM + +source_urls = ["https://github.com/PacificBiosciences/%(namelower)s"] +sources = ["releases/download/v%(version)s/%(namelower)s3"] +checksums = ["3d012810dc4cb54f89a7c80b26fc5f27da26c11f7ad6062cab462a6c691678f7"] + +extract_sources = False + +postinstallcmds = [ + "cp %(builddir)s/releases/download/v%(version)s/%(namelower)s* %(installdir)s" +] + +sanity_check_paths = { + "files": [ + "isoseq3", + ], + "dirs": [""], +} + +sanity_check_commands = ['isoseq3 --version'] + +moduleclass = "bio" diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2023.03.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2023.03.eb new file mode 100644 index 000000000000..0bb3e2c0aba6 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2023.03.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2023.03' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2023.1.0' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.9.0', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iimpi-2023.03.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iimpi-2023.03.eb new file mode 100644 index 000000000000..3809bf2daac1 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2023.1.0-iimpi-2023.03.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2023.1.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2023.03'} + +dependencies = [('imkl', version, '', SYSTEM)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.1.0.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0.eb new file mode 100644 index 000000000000..2dd371edc01c --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2023.1.0.eb @@ -0,0 +1,18 @@ +name = 'imkl' +version = '2023.1.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/cd17b7fe-500e-4305-a89b-bd5b42bfd9f8/'] +sources = ['l_onemkl_p_%(version)s.46342_offline.sh'] +checksums = ['cc28c94cab23c185520b93c5a04f3979d8da6b4c90cee8c0681dd89819d76167'] + +interfaces = False + +installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2021.9.0-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/i/impi/impi-2021.9.0-intel-compilers-2023.1.0.eb new file mode 100644 index 000000000000..6e886d07ac18 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.9.0-intel-compilers-2023.1.0.eb @@ -0,0 +1,16 @@ +name = 'impi' +version = '2021.9.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/718d6f8f-2546-4b36-b97b-bc58d5482ebf/'] +sources = ['l_mpi_oneapi_p_%(version)s.43482_offline.sh'] +checksums = ['5c170cdf26901311408809ced28498b630a494428703685203ceef6e62735ef8'] + +dependencies = [('UCX', '1.14.0')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.2-foss-2022a.eb b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.2-foss-2022a.eb new file mode 100644 index 000000000000..58e1804543bb --- /dev/null +++ b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.2-foss-2022a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'infercnvpy' +version = '0.4.2' + +homepage = 'https://github.com/icbi-lab/infercnvpy' +description = "Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('tqdm', '4.64.0'), + ('IPython', '8.5.0'), + ('leidenalg', '0.9.1'), + ('scanpy', '1.9.1'), + ('polars', '0.15.6'), # required by gtfparse +] + +use_pip = True + +# avoid hatchling requirement to install infercnvpy +# (since installing it introduces conflicting version requirements with poetry included with Python) +local_preinstallopts = """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """ +local_preinstallopts += """-e 's/^requires = .*/requires = ["setuptools"]/g' """ +local_preinstallopts += r"""-e 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """ + +exts_list = [ + ('setuptools', '67.6.1', { + 'checksums': ['257de92a9d50a60b8e22abfcbb771571fde0dbf3ec234463212027a4eeecbe9a'], + }), + ('gtfparse', '2.0.1', { + 'checksums': ['c45439af58cb48120910bebe4625371d8fb5735f12a749e8933c9d6f2b1a558c'], + }), + ('pyreadr', '0.4.7', { + 'checksums': ['901110d62b4bedaef288f4db81425fb696edc721fe2c34c1083f5fb11050a73c'], + }), + ('session-info', '1.0.0', { + 'sources': ['session_info-%(version)s.tar.gz'], + 'checksums': ['3cda5e03cca703f32ae2eadbd6bd80b6c21442cfb60e412c21cb8ad6d5cbb6b7'], + }), + (name, version, { + 'checksums': ['3cfd23afc2dbbca3508a305032c032440d2af292d037d43a7b5046c7bd36ed22'], + 'preinstallopts': local_preinstallopts, + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.1.0.eb new file mode 100644 index 000000000000..91d2ec40b6e5 --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2023.1.0.eb @@ -0,0 +1,37 @@ +name = 'intel-compilers' +version = '2023.1.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/89283df8-c667-47b0-b7e1-c4573e37bd3e/', + ], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.46347_offline.sh', + }, + { + 'source_urls': [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/150e0430-63df-48a0-8469-ecebff0a1858/', + ], + 'filename': 'l_fortran-compiler_p_%(version)s.46348_offline.sh', + }, +] +checksums = [ + {'l_dpcpp-cpp-compiler_p_2023.1.0.46347_offline.sh': + '3ac1c1179501a2646cbb052b05426554194573b4f8e2344d7699eed03fbcfa1d'}, + {'l_fortran-compiler_p_2023.1.0.46348_offline.sh': + '7639af4b6c928e9e3ba92297a054f78a55f4f4d0db9db0d144cc6653004e4f24'}, +] + +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/intel/intel-2023.03.eb b/easybuild/easyconfigs/i/intel/intel-2023.03.eb new file mode 100644 index 000000000000..9c71d4bc13ea --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2023.03.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2023.03' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2023.1.0' +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.9.0', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', SYSTEM), + ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2022a.eb b/easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2022a.eb new file mode 100644 index 000000000000..0d3dd0f948f0 --- /dev/null +++ b/easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'ipympl' +version = '0.9.3' + +homepage = 'https://matplotlib.org/ipympl' +description = """Leveraging the Jupyter interactive widgets framework, ipympl enables the +interactive features of matplotlib in the Jupyter notebook and in JupyterLab. +Besides, the figure canvas element is a proper Jupyter interactive widget which +can be positioned in interactive widget layouts. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('JupyterLab', '3.5.0'), + ('matplotlib', '3.5.2'), + ('Pillow', '9.1.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['d113cd55891bafe9b27ef99b6dd111a87beb6bb2ae550c404292272103be8013'], + }), +] + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb index c83e203d15d0..5c8c24efaf6b 100644 --- a/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb +++ b/easybuild/easyconfigs/i/ispc/ispc-1.10.0.eb @@ -13,9 +13,9 @@ description = """Intel SPMD Program Compilers; An open-source compiler for high- toolchain = SYSTEM -sources = ['ispc-v%(version)s-linux.tar.gz'] -source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')] -checksums = ['453211ade91c33826f4facb1336114831adbd35196d016e09d589a6ad8699aa3'] +source_urls = ['https://github.com/ispc/ispc/releases/download/v%(version)s/'] +sources = ['ispc-v%(version)sb-linux.tar.gz'] +checksums = ['7fbcf27be161d80a28ab258b3beef3f137a72ac4edc9aa92b1cca044521ff6ca'] sanity_check_paths = { 'files': ["bin/ispc"], diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.12.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.12.0.eb index 450f335d81a0..cb286e829488 100644 --- a/easybuild/easyconfigs/i/ispc/ispc-1.12.0.eb +++ b/easybuild/easyconfigs/i/ispc/ispc-1.12.0.eb @@ -13,9 +13,9 @@ description = """Intel SPMD Program Compilers; An open-source compiler for high- toolchain = SYSTEM -source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')] -sources = ['ispc-v%(version)s-linux.tar.gz'] -checksums = ['79decaef42bc5433ab30f5879eb91af14473a42e8b51ec727a97f61ee918497e'] +source_urls = ['https://github.com/ispc/ispc/releases/download/v%(version)s/'] +sources = ['ispc-v%(version)sb-linux.tar.gz'] +checksums = ['7a2bdd5fff5c1882639cfbd66bca31dbb68c7177f3013e80b0813a37fe0fdc23'] sanity_check_paths = { 'files': ["bin/ispc"], diff --git a/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb b/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb index b266d99faac3..0b7e085e0e3d 100644 --- a/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb +++ b/easybuild/easyconfigs/i/ispc/ispc-1.6.0.eb @@ -13,8 +13,9 @@ description = """Intel SPMD Program Compilers; An open-source compiler for high- toolchain = SYSTEM +source_urls = ['https://github.com/ispc/ispc/releases/download/v%(version)s/'] sources = ['ispc-v%(version)s-linux.tar.gz'] -source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')] +checksums = ['67abd92645ead651ced74c4e358313414f5786f0275d975ef4888f168ca342d1'] sanity_check_paths = { 'files': ["ispc"], diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..1568d4b64e4f --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '4.0.0' + +homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' + +description = """ + The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in + the JPEG-2000 Part-1 standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'jasper-software' +source_urls = [GITHUB_SOURCE] +sources = ['version-%(version)s.tar.gz'] +checksums = ['977c4c2e4210f4e37313cd2232d99e73d57ab561917b3c060bcdd5e83a0a13f1'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +configopts = '-DJAS_ENABLE_DOC=OFF ' + +sanity_check_paths = { + 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], + 'dirs': ['include'], +} + +sanity_check_commands = ['jasper --version'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/Java/Java-11.0.18.eb b/easybuild/easyconfigs/j/Java/Java-11.0.18.eb new file mode 100644 index 000000000000..c41c7c582f90 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-11.0.18.eb @@ -0,0 +1,30 @@ +name = 'Java' +version = '11.0.18' +local_build = '10' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version)s_%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' + % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + '4a29efda1d702b8ff38e554cf932051f40ec70006caed5c4857a8cbc7a0b7db7', + local_tarball_tmpl % ('aarch64', local_build): + '04d5eeff6a6449bcdca0f52cd97bafd43ce09d40ef1e73fa0e1add63bea4a9c8', + local_tarball_tmpl % ('ppc64le', local_build): + '459148d489b08ceec2d901e950ac36722b4c55e907e979291ddfc954ebdcea47', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-11.eb b/easybuild/easyconfigs/j/Java/Java-11.eb index d53c0b9b2f5e..77086a3e1b8c 100644 --- a/easybuild/easyconfigs/j/Java/Java-11.eb +++ b/easybuild/easyconfigs/j/Java/Java-11.eb @@ -9,6 +9,6 @@ Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [('Java', '%(version)s.0.16')] +dependencies = [('Java', '%(version)s.0.18')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-17.0.6.eb b/easybuild/easyconfigs/j/Java/Java-17.0.6.eb new file mode 100644 index 000000000000..71d89858ea44 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-17.0.6.eb @@ -0,0 +1,30 @@ +name = 'Java' +version = '17.0.6' +local_build = '10' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version)s_%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' + % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + 'a0b1b9dd809d51a438f5fa08918f9aca7b2135721097f0858cf29f77a35d4289', + local_tarball_tmpl % ('aarch64', local_build): + '9e0e88bbd9fa662567d0c1e22d469268c68ac078e9e5fe5a7244f56fec71f55f', + local_tarball_tmpl % ('ppc64le', local_build): + 'cb772c3fdf3f9fed56f23a37472acf2b80de20a7113fe09933891c6ef0ecde95', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-17.eb b/easybuild/easyconfigs/j/Java/Java-17.eb index b5936b5a1548..1efea31e8434 100644 --- a/easybuild/easyconfigs/j/Java/Java-17.eb +++ b/easybuild/easyconfigs/j/Java/Java-17.eb @@ -9,6 +9,6 @@ Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [('Java', '%(version)s.0.4')] +dependencies = [('Java', '%(version)s.0.6')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-8.362.eb b/easybuild/easyconfigs/j/Java/Java-8.362.eb new file mode 100644 index 000000000000..f8c6b809aa0a --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-8.362.eb @@ -0,0 +1,31 @@ +name = 'Java' +version = '8.362' +local_build = 'b09' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK8U-jdk_%s_linux_hotspot_%%(version_major)su%%(version_minor)s%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin8-binaries/releases/download/' + 'jdk%%(version_major)su%%(version_minor)s-%s/' % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + '1486a792fb224611ce0cd0e83d4aacd3503b56698549f8e9a9f0a6ebb83bdba1', + local_tarball_tmpl % ('aarch64', local_build): + '9290a8beefd7a94f0eb030f62d402411a852100482b9c5b63714bacc57002c2a', + local_tarball_tmpl % ('ppc64le', local_build): + '69658dd316c6a160915655971573179766e19c6610ea03880c1e578a0e518f74', + + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-8.eb b/easybuild/easyconfigs/j/Java/Java-8.eb index 8c9091f83dd0..854eccb56cb8 100644 --- a/easybuild/easyconfigs/j/Java/Java-8.eb +++ b/easybuild/easyconfigs/j/Java/Java-8.eb @@ -9,6 +9,6 @@ Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [('Java', '%(version)s.345')] +dependencies = [('Java', '%(version)s.362')] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..29e5a68235b0 --- /dev/null +++ b/easybuild/easyconfigs/j/Judy/Judy-1.0.5-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Judy' +version = '1.0.5' + +homepage = 'http://judy.sourceforge.net/' +description = "A C library that implements a dynamic array." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['http://downloads.sourceforge.net/judy'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['Judy-1.0.5_parallel-make.patch'] # fix Make dependencies, so parallel build also works + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.39'), +] +checksums = [ + 'd2704089f85fdb6f2cd7e77be21170ced4b4375c03ef1ad4cf1075bd414a63eb', # Judy-1.0.5.tar.gz + '14c2eba71088f3db9625dc4605c6d7183d72412d75ef6c9fd9b95186165cf009', # Judy-1.0.5_parallel-make.patch +] + +preconfigopts = "sed -i 's/AM_CONFIG_HEADER/AC_CONFIG_HEADERS/g' configure.ac && " +preconfigopts += "autoreconf -i && " + +configopts = '--enable-shared --enable-static' + +sanity_check_paths = { + 'files': ["include/%(name)s.h", "lib/lib%(name)s.a", "lib/lib%(name)s.la", "lib/lib%%(name)s.%s" % SHLIB_EXT], + 'dirs': ["share/man"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb index 9f427a4cb205..4addecfb2d62 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-3.0.0-GCCcore-11.3.0.eb @@ -19,7 +19,8 @@ dependencies = [ ('Mako', '1.2.0'), ('configurable-http-proxy', '4.5.3'), ('OpenSSL', '1.1', '', SYSTEM), - ('jupyter-server-proxy', '3.2.2') # This is optional, but commonly used together + ('jupyter-server-proxy', '3.2.2'), # optional, but commonly used together + ('PycURL', '7.45.2'), # optional, recommended with large number of users ] use_pip = True diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..4ddfd6746ecc --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,130 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.3.25' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Bazel', '5.1.1'), + ('pytest-xdist', '2.5.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.36.0', '-nodocs'), + ('matplotlib', '3.5.2'), # required for tests/lobpcg_test.py +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM), + ('NCCL', '2.12.12', versionsuffix), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('flatbuffers-python', '2.0'), +] + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in WORKSPACE +local_tf_commit = 'f0fe8d4c04fab1f157854a1aa3c136377901cdef' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '1.3.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['463c38a08d2e4cef6c498b76ba5bd4858e4c6ef51da1a5a1f27139a022e20248'], + }), + ('jaxlib', version, { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir), + ], + 'checksums': [ + # jaxlib-v0.3.25.tar.gz + '73ebc7868631cd9d520385557bbd7f08762d748a5a6a1bebef0f3b8d7ba748ef', + # tensorflow-f0fe8d4c04fab1f157854a1aa3c136377901cdef.tar.gz + '9ebba3031e8a81993682e4b9e43891ebb8480b6287e635df8e7efaa45ab5ede7', + # jaxlib_local-tensorflow-repo.sed + 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', + # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch + '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('etils', '0.8.0', { + 'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'], + }), + (name, version, { + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'patches': [ + 'jax-0.3.23_relax-testPoly5-tolerance.patch', + 'jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch', + 'jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch', + 'jax-0.4.4_cusparse.patch', + ], + 'checksums': [ + {'jax-v0.3.25.tar.gz': '49e8ce88ddd7dd0de86116c9d75d98a577a9061377ec423493fbac5ea29f79f0'}, + {'jax-0.3.23_relax-testPoly5-tolerance.patch': + 'be64bf36dde4884a97b6c8bb22c6b14ab5b24033cd40bfe7ce18363c55c30e87'}, + {'jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch': + '70f16f2dba03ab162ce6e13ea61774524b485e9630209bbd4bec81fd16c8812f'}, + {'jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch': + '335a8e206d14338176bf4136a131afe5d7b75999ac2c67f0ae79031322e25936'}, + {'jax-0.4.4_cusparse.patch': '7414115533cce9f37c60850c09c69563a0ed6477c73f03c4132b9c2ae75ae60f'}, + ], + # deliberately not testing in parallel, as that results in (additional) failing tests; + # use XLA_PYTHON_CLIENT_ALLOCATOR=platform to allocate and deallocate GPU memory during testing, + # see https://github.com/google/jax/issues/7323 and + # https://github.com/google/jax/blob/main/docs/gpu_memory_allocation.rst; + # use CUDA_VISIBLE_DEVICES=0 to avoid failing tests on systems with multiple GPUs; + # use NVIDIA_TF32_OVERRIDE=0 to avoid lossing numerical precision by disabling TF32 Tensor Cores; + 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 XLA_PYTHON_CLIENT_ALLOCATOR=platform " + + "JAX_ENABLE_X64=true pytest -vv tests", + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a.eb new file mode 100644 index 000000000000..fb821e58e1d0 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.25-foss-2022a.eb @@ -0,0 +1,114 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.3.25' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Bazel', '5.1.1'), + ('pytest-xdist', '2.5.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.36.0', '-nodocs'), + ('matplotlib', '3.5.2'), # required for tests/lobpcg_test.py +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('flatbuffers-python', '2.0'), +] + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in WORKSPACE +local_tf_commit = 'f0fe8d4c04fab1f157854a1aa3c136377901cdef' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '1.3.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['463c38a08d2e4cef6c498b76ba5bd4858e4c6ef51da1a5a1f27139a022e20248'], + }), + ('jaxlib', version, { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir), + ], + 'checksums': [ + # jaxlib-v0.3.25.tar.gz + '73ebc7868631cd9d520385557bbd7f08762d748a5a6a1bebef0f3b8d7ba748ef', + # tensorflow-f0fe8d4c04fab1f157854a1aa3c136377901cdef.tar.gz + '9ebba3031e8a81993682e4b9e43891ebb8480b6287e635df8e7efaa45ab5ede7', + # jaxlib_local-tensorflow-repo.sed + 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', + # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch + '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('etils', '0.8.0', { + 'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'], + }), + (name, version, { + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'patches': [ + 'jax-0.3.23_relax-testPoly5-tolerance.patch', + 'jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch', + ], + 'checksums': [ + {'jax-v0.3.25.tar.gz': '49e8ce88ddd7dd0de86116c9d75d98a577a9061377ec423493fbac5ea29f79f0'}, + {'jax-0.3.23_relax-testPoly5-tolerance.patch': + 'be64bf36dde4884a97b6c8bb22c6b14ab5b24033cd40bfe7ce18363c55c30e87'}, + {'jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch': + '70f16f2dba03ab162ce6e13ea61774524b485e9630209bbd4bec81fd16c8812f'}, + ], + 'runtest': "pytest -n %(parallel)s tests", + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch b/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch new file mode 100644 index 000000000000..50eef092964f --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-qdwh-test-rank-deficient-deficient.patch @@ -0,0 +1,14 @@ +This test is known to fail on certain CPU arquitectures +see https://github.com/google/jax/issues/14793 +author: Alex Domingo (Vrije Universiteit Brussel) +--- tests/qdwh_test.py.orig 2023-04-06 10:38:07.838718000 +0200 ++++ tests/qdwh_test.py 2023-04-06 10:38:24.168026081 +0200 +@@ -168,7 +168,7 @@ + [dict(m=m, n=n) for m, n in [(10, 10), (8, 8)]], + log_cond=np.linspace(1, 4, 4), + ) +- def testQdwhWithOnRankDeficientInput(self, m, n, log_cond): ++ def disabled_testQdwhWithOnRankDeficientInput(self, m, n, log_cond): + """Tests qdwh with rank-deficient input.""" + a = jnp.triu(jnp.ones((m, n))).astype(_QDWH_TEST_DTYPE) + diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch b/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch new file mode 100644 index 000000000000..8a70ed941cf2 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.25_skip-test-bcoo-dot-general-cusparse.patch @@ -0,0 +1,14 @@ +Skip flaky tests with cuSPARSE as its API is quite variable, +might solve itself in future versions of CUDA or jax +see https://github.com/google/jax/issues/14663 +author: Alex Domingo (Vrije Universiteit Brussel) +--- tests/sparse_test.py.orig 2023-04-06 23:41:58.192895000 +0200 ++++ tests/sparse_test.py 2023-04-06 23:59:56.319161821 +0200 +@@ -1173,6 +1173,7 @@ + ], + dtype=jtu.dtypes.floating + jtu.dtypes.complex, + ) ++ @unittest.skip("CUSPARSE_OPERATION_NON_TRANSPOSE is not supported with CUSPARSE_SPMM_COO_ALG2 on CUDA 11.7.0") + def test_bcoo_dot_general_cusparse( + self, lhs_shape, rhs_shape, dtype, lhs_contracting, rhs_contracting): + rng = jtu.rand_small(self.rng()) diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..b6086a982622 --- /dev/null +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'jbigkit' +version = '2.1' + +homepage = 'https://www.cl.cam.ac.uk/~mgk25/jbigkit/' +description = """JBIG-KIT is a software implementation of the JBIG1 data + compression standard (ITU-T T.82), which was designed for bi-level image + data, such as scanned documents.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cl.cam.ac.uk/~mgk25/jbigkit/download'] +sources = [SOURCE_TAR_GZ] +patches = [ + '%(name)s-%(version)s_libpath.patch', + '%(name)s-%(version)s_shlib.patch', +] +checksums = [ + {'jbigkit-2.1.tar.gz': 'de7106b6bfaf495d6865c7dd7ac6ca1381bd12e0d81405ea81e7f2167263d932'}, + {'jbigkit-2.1_libpath.patch': '97c88956090097b484fcdb90e12eab82212e67ddc862f035d7c6446a696786ce'}, + {'jbigkit-2.1_shlib.patch': '54ae429e8ec949eceee0f902b676f572f1cdfbff46f77c7222acdeafb643a696'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +files_to_copy = [ + (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), + (['libjbig/jbig85.h', 'libjbig/jbig.h', 'libjbig/jbig_ar.h'], 'include'), + (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), +] + +sanity_check_paths = { + 'files': ['lib/libjbig85.a', 'lib/libjbig.a', + 'bin/pbmtojbg', 'bin/jbgtopbm', + 'include/jbig.h', 'include/jbig_ar.h', + ], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..aae1125cf83c --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-5.3.0-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '5.3.0' + +homepage = 'http://jemalloc.net' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/jemalloc/jemalloc/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['ef6f74fd45e95ee4ef7f9e19ebe5b075ca6b7fbe0140612b2a161abafb7ee179'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.39'), +] + +# From version 5.2.1 (or maybe earlier) it does no longer build, +# nor try to install, documentation if xsltproc is missing. +# So we can use normal installation. +preconfigopts = "./autogen.sh && " +configopts = "--with-version=%(version)s-0-g0000 " # build with version info + +sanity_check_paths = { + 'files': ['bin/jeprof', 'lib/libjemalloc.a', 'lib/libjemalloc_pic.a', 'lib/libjemalloc.%s' % SHLIB_EXT, + 'include/jemalloc/jemalloc.h'], + 'dirs': [], +} + +# jemalloc can be used via $LD_PRELOAD, but we don't enable this by +# default, you need to opt-in to it +# modextrapaths = {'LD_PRELOAD': ['lib/libjemalloc.%s' % SHLIB_EXT]} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..50a777efb878 --- /dev/null +++ b/easybuild/easyconfigs/j/json-c/json-c-0.16-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'json-c' +version = '0.16' +local_suff = '-20220414' + +homepage = 'https://github.com/json-c/json-c' +description = """JSON-C implements a reference counting object model that allows you to easily construct JSON objects + in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON +objects.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/json-c/json-c/archive/'] +sources = ['json-c-%%(version)s%s.tar.gz' % local_suff] +checksums = ['3ecaeedffd99a60b1262819f9e60d7d983844073abc74e495cb822b251904185'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +# disable using Valgrind during the tests to avoid failures caused by using an OS Valgrind +pretestopts = 'USE_VALGRIND=0 ' +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libjson-c.a', 'lib/libjson-c.%s' % SHLIB_EXT, 'lib/pkgconfig/json-c.pc'], + 'dirs': ['include/json-c'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..37c5915ff8ee --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2-GCCcore-10.3.0.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-resource-usage' +version = '0.6.2' + +homepage = 'https://github.com/jupyter-server/jupyter-resource-usage' +description = """Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or CPU)""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('IPython', '7.25.0'), +] + +use_pip = True + +exts_list = [ + ('websocket-client', '1.4.1', { + 'modulename': 'websocket', + 'checksums': ['f9611eb65c8241a67fb373bef040b3cf8ad377a9f6546a12b620b6511e8ea9ef'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.1', { + 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], + }), + ('requests-unixsocket', '0.3.0', { + 'checksums': ['28304283ea9357d45fff58ad5b11e47708cfbf5806817aa59b2a363228ee971e'], + }), + ('jupyter_server', '1.11.1', { + 'checksums': ['ab7ab1cc38512f15026cbcbb96300fb46ec8b24aa162263d9edd00e0a749b1e8'], + }), + (name, version, { + 'patches': [ + 'jupyter-resource-usage-0.6.1_compatibility.patch', + 'jupyter-resource-usage-0.6.2_fix_update_cpu.patch', + ], + 'checksums': [ + '735acfe9516c68d1f50c25f74b236075da2adde49f734b24f6d2578ab9aa8d0c', # jupyter-resource-usage-0.6.2.tar.gz + # jupyter-resource-usage-0.6.1_compatibility.patch + 'b030065413bac04bd40088cd92be98bac3e92d68189d03d338986444af3953f4', + # jupyter-resource-usage-0.6.2_fix_update_cpu.patch + 'e2d2ea15211c90faebb57c1170a105f94fe0fd28055a69969dd53dad9ff7f990', + ], + }), +] + +# Add the notebook extension to the search path for jupyter notebooks +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter/', +} + +sanity_check_paths = { + 'dirs': [ + 'lib/python%(pyshortver)s/site-packages/jupyter_resource_usage', + 'lib/python%(pyshortver)s/site-packages/jupyter_server' + ], + 'files': ['bin/jupyter-server'], +} + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2_fix_update_cpu.patch b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2_fix_update_cpu.patch new file mode 100644 index 000000000000..181500591a53 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-0.6.2_fix_update_cpu.patch @@ -0,0 +1,16 @@ +# Author: Caspar van Leeuwen, SURF +# If the CPU was idle (i.e. cpuPercent=0), the display showing CPU usage wouldn't update, +# because of a faulty logic. This patch fixes that. +# See https://github.com/jupyter-server/jupyter-resource-usage/pull/147 +diff -Nru jupyter-resource-usage-0.6.2.orig/jupyter_resource_usage/static/main.js jupyter-resource-usage-0.6.2/jupyter_resource_usage/static/main.js +--- jupyter-resource-usage-0.6.2.orig/jupyter_resource_usage/static/main.js 2022-09-30 19:02:36.892711996 +0200 ++++ jupyter-resource-usage-0.6.2/jupyter_resource_usage/static/main.js 2022-09-30 19:02:59.994787990 +0200 +@@ -74,7 +74,7 @@ + + // Handle CPU display + var cpuPercent = data['cpu_percent']; +- if (cpuPercent) { ++ if (cpuPercent !== undefined) { + // Remove hide CSS class if the metrics API gives us a CPU percent to display + $('#jupyter-resource-usage-display-cpu').removeClass('jupyter-resource-usage-hide'); + var maxCpu = data['cpu_count']; diff --git a/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..552befac6557 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-11.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'jupyterlmod' +version = '4.0.3' + +# This easyconfig installs the notebook and lab extension of Jupyter Lmod + +homepage = 'https://github.com/cmd-ntrf/jupyter-lmod' +description = """Jupyter interactive notebook server extension that allows users to interact with +environment modules before launching kernels. The extension uses Lmod's Python +interface to accomplish module-related tasks like loading, unloading, saving +collections, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), + ('jupyter-server', '1.21.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'sources': ['%(name)s-%(version)s-py3-none-any.whl'], + 'checksums': ['9939bd7927c2c347f9884247bac58018ca44d56184c5f29e9d704a9b3a09a299'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'share/jupyter'], +} + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..fda9c28356f5 --- /dev/null +++ b/easybuild/easyconfigs/k/Kalign/Kalign-3.3.5-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +# Contribution from the NIHR Biomedical Research Centre +easyblock = 'CMakeMake' + +name = 'Kalign' +version = '3.3.5' + +homepage = 'https://github.com/TimoLassmann/kalign' +description = "Kalign is a fast multiple sequence alignment program for biological sequences." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/TimoLassmann/kalign/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['75f3a127d2a9eef1eafd931fb0785736eb3f82826be506e7edd00daf1ba26212'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['bin/kalign'], + 'dirs': [], +} + +sanity_check_commands = ["kalign --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb new file mode 100644 index 000000000000..f8e15be69549 --- /dev/null +++ b/easybuild/easyconfigs/k/Keras/Keras-2.4.3-fosscuda-2020b-TensorFlow-2.5.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'Keras' +version = '2.4.3' +local_tf_version = '2.5.0' +versionsuffix = '-TensorFlow-2.5.0' + +homepage = 'https://keras.io/' +description = """ +Keras is a deep learning API written in Python, running on top of the machine learning platform TensorFlow. +""" + +toolchain = {'name': 'fosscuda', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('Theano', '1.1.2', '-PyMC'), + ('PyYAML', '5.3.1'), + ('TensorFlow', local_tf_version), # provides h5py 2.1.0 +] + +use_pip = True + +exts_list = [ + ('Keras_Applications', '1.0.8', { + 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + (name, version, { + 'checksums': ['fedd729b52572fb108a98e3d97e1bac10a81d3917d2103cc20ab2a5f03beb973'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb new file mode 100644 index 000000000000..9ed7324537c9 --- /dev/null +++ b/easybuild/easyconfigs/k/Kraken2/Kraken2-2.1.2-gompi-2022a.eb @@ -0,0 +1,70 @@ +easyblock = 'PackedBinary' + +name = 'Kraken2' +version = '2.1.2' + +homepage = 'https://github.com/DerrickWood/kraken2/wiki' +description = """Kraken is a system for assigning taxonomic labels to short DNA sequences, + usually obtained through metagenomic studies. Previous attempts by other + bioinformatics software to accomplish this task have often used sequence + alignment or machine learning techniques that were quite slow, leading to + the development of less sensitive but much faster abundance estimation + programs. Kraken aims to achieve high sensitivity and high speed by + utilizing exact alignments of k-mers and a novel classification algorithm.""" + +# part is compiled with $CXX, the rest is in Perl +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'openmp': True, 'cstd': 'c++11'} + +github_account = 'DerrickWood' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-2.1.1_fix_installation_for_easybuild.patch', + '%(name)s-%(version)s_fix_ncbi_https_server.patch', +] +checksums = [ + 'e5f431e8bc3d5493a79e1d8125f4aacbad24f9ea2cc9657b66da06a32bef6ff3', # v2.1.2.tar.gz + # Kraken2-2.1.1_fix_installation_for_easybuild.patch + '5ea9093becbdf7705a29fd2e56050118700c850ac5374aae5ee9b5e5924d3a11', + '8db78096340352e97589a189a86a020ff31bd60f0c332a1794d532fabd5bd116', # Kraken2-2.1.2_fix_ncbi_https_server.patch +] + +dependencies = [ + ('Perl', '5.34.1'), + ('BLAST+', '2.13.0'), + ('wget', '1.21.3'), +] + +install_cmd = 'cd %(builddir)s/%(namelower)s-%(version)s && ' +install_cmd += './install_kraken2.sh %(installdir)s/bin' + +# Kraken2 databases can be downloaded from https://benlangmead.github.io/aws-indexes/k2 +# or built as described in https://github.com/DerrickWood/kraken2/wiki/Manual#kraken-2-databases +# The following commands will build and install the standard databases (100GB) in local_db_path +# local_db_path = '%(installdir)s/db' +# postinstallcmds = [ +# 'mkdir %s' % local_db_path, +# 'cd %%(installdir)s/bin && ./kraken2-build --standard --threads %%(parallel)s --db %s' % local_db_path, +# ] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in [ + '16S_gg_installation.sh', '16S_rdp_installation.sh', '16S_silva_installation.sh', 'add_to_library.sh', + 'build_db', 'build_gg_taxonomy.pl', 'build_kraken2_db.sh', 'build_rdp_taxonomy.pl', 'build_silva_taxonomy.pl', + 'classify', 'clean_db.sh', 'cp_into_tempfile.pl', 'download_genomic_library.sh', 'download_taxonomy.sh', + 'dump_table', 'estimate_capacity', 'kraken2', 'kraken2-build', 'kraken2-inspect', 'kraken2lib.pm', + 'lookup_accession_numbers.pl', 'make_seqid2taxid_map.pl', 'mask_low_complexity.sh', 'rsync_from_ncbi.pl', + 'scan_fasta_file.pl']], + 'dirs': [], +} + +sanity_check_commands = [ + 'kraken2 --help', + 'kraken2-build --help', + 'kraken2-inspect --help', + 'build_db -h', + 'classify -h', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb new file mode 100644 index 000000000000..7e0b6557dddb --- /dev/null +++ b/easybuild/easyconfigs/k/KrakenUniq/KrakenUniq-1.0.3-GCC-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'Binary' + +name = 'KrakenUniq' +version = '1.0.3' + +homepage = 'https://github.com/fbreitwieser/krakenuniq/' +description = """KrakenUniq: confident and fast metagenomics classification using unique k-mer counts""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'fbreitwieser' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['559b45081688118b4872e1b9153f83d0ae3414649a1b299ab4f9996d9e154403'] + +dependencies = [ + ('Jellyfish', '2.3.0'), + ('Perl', '5.34.1'), + ('bzip2', '1.0.8'), + ('Compress-Raw-Zlib', '2.202'), +] + +extract_sources = True + +install_cmd = './install_krakenuniq.sh -l %(installdir)s/bin %(installdir)s ' + +sanity_check_commands = [ + 'krakenuniq --version', + 'krakenuniq-download --db %(installdir)s/DBDIR taxonomy && rm -r %(installdir)s/DBDIR' +] +sanity_check_paths = { + 'files': ['bin/krakenuniq', 'bin/krakenuniq-build', 'bin/krakenuniq-report'], + 'dirs': ['bin'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LIANA/LIANA-0.1.11-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/l/LIANA/LIANA-0.1.11-foss-2022a-R-4.2.1.eb new file mode 100644 index 000000000000..2584ae7e67fa --- /dev/null +++ b/easybuild/easyconfigs/l/LIANA/LIANA-0.1.11-foss-2022a-R-4.2.1.eb @@ -0,0 +1,56 @@ +easyblock = 'Bundle' + +name = 'LIANA' +version = '0.1.11' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://saezlab.github.io/liana/' +description = """LIANA: a LIgand-receptor ANalysis frAmework. LIANA enables the use of any + combination of ligand-receptor methods and resources, and their consensus.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + 'https://bioconductor.org/packages/release/bioc/src/contrib/' # contrib for Bioconductor packages +] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': source_urls, +} + +exts_list = [ + ('rlang', '1.0.4', { + 'checksums': ['1fb789d46c6a855ce37eba63c353b85aa600c4a2a7ca6075f2632540b42a8696'], + }), + ('tidyselect', '1.2.0', { + 'checksums': ['538d26b727e37d618e2efd3b00836048f103112a03e6994bf07a02392e269e3b'], + }), + ('OmnipathR', '3.8.0', { + 'checksums': ['0e12ea562e135a8c670b5b4ec4000463c9ee12bd6d957bfcc2db36b5ecd85664'], + }), + (name, version, { + 'source_urls': ['https://github.com/saezlab/liana/archive/refs/tags/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['fd866f4b66ee3d98c63f43d5437527c541ce624fe303a2ee2fdb729770afa91e'], + 'modulename': 'liana' + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['liana'], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..c13e24fcc530 --- /dev/null +++ b/easybuild/easyconfigs/l/LSD2/LSD2-2.3-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +# Updated to v2.3 by +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'LSD2' +version = '2.3' + +homepage = 'https://github.com/tothuhien/lsd2' +description = "Least-squares methods to estimate rates and dates from phylogenies" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'tothuhien' + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v.%(version)s.tar.gz'] +patches = ['%(name)s-1.9.7_fix_cmake_to_build_lib_and_binary.patch'] +checksums = [ + 'c7819be1204ebf77e3660bba91dbd8629ba9437216814f276a11b9156dbb0649', # v.2.3.tar.gz + # LSD2-1.9.7_fix_cmake_to_build_lib_and_binary.patch + '8ef6e8c3a9a5aa2099678ed84a7e54ef687e3900894694c4eec1f5399f0487f6', +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/lsd2', 'lib/liblsd2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..e1ced572aa53 --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'https://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.39')] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..38c850b17e8e --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'https://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.40')] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-11.3.0.eb b/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-11.3.0.eb new file mode 100644 index 000000000000..59d93ffd865b --- /dev/null +++ b/easybuild/easyconfigs/l/L_RNA_scaffolder/L_RNA_scaffolder-20190530-GCC-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'L_RNA_scaffolder' +local_commit = '98f19e3' +version = '20190530' + +homepage = 'https://github.com/CAFS-bioinformatics/L_RNA_scaffolder' +description = "L_RNA_scaffolder is a genome scaffolding tool with long trancriptome reads" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/CAFS-bioinformatics/L_RNA_scaffolder/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['ef4c5bf3511e9947bdb33201bdcaf1ff779ca315a2139f73bb549fb6bfc05f5a'] + +dependencies = [ + ('BioPerl', '1.7.8'), +] + +fix_perl_shebang_for = ['*.pl'] + +postinstallcmds = ["chmod a+x %(installdir)s/L_RNA_scaffolder.sh"] + +sanity_check_paths = { + 'files': ['calculate-lc', 'calculate-pid', 'convert', 'convert_linker', 'count_connection_frequency', + 'delete_block', 'delete_linker', 'delete_same_fragment', 'filter_scaffold.pl', + 'find_end_node', 'find_reliable_connection', 'find_start_node', 'form_block', + 'form_path.pl', 'generate_scaffold.pl', 'generate_unscaffold.pl', 'L_RNA_scaffolder.sh', 'link_block', + 'order', 'overlap', 'route.pl', 'search_guider', 'select_nodes'], + 'dirs': [], +} + +sanity_check_commands = ["L_RNA_scaffolder.sh -? | grep '^Usage: sh L_RNA_scaffolder.sh'"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..9d9e6c1971cc --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.5.0' + +homepage = 'https://libtiff.gitlab.io/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/libtiff/'] +sources = ['tiff-%(version)s.tar.gz'] +checksums = ['c7a1d9296649233979fa3eacffef3fa024d73d05d589cb622727b5b08c423464'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('zlib', '1.2.13'), + ('libjpeg-turbo', '2.1.5.1'), + ('XZ', '5.4.2'), + ('jbigkit', '2.1'), + ('zstd', '1.5.5'), + ('libdeflate', '1.18'), +] + +configopts = "--enable-ld-version-script " +configopts += "--disable-webp --disable-sphinx " + +sanity_check_paths = { + 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, + 'lib/libtiffxx.a', 'lib/libtiffxx.%s' % SHLIB_EXT, 'lib/pkgconfig/libtiff-4.pc'], + 'dirs': [], +} + +sanity_check_commands = ["tiffinfo -h"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb new file mode 100644 index 000000000000..9de77dd4e7b8 --- /dev/null +++ b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9-gompi-2022a.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'LoRDEC' +version = '0.9' + +homepage = 'https://www.lirmm.fr/~rivals/lordec' +description = """Program for correcting sequencing errors in long reads (e.g., PacBio, Oxford Nanopore) using highly +accurate short reads (e.g., Illumina).""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://gite.lirmm.fr/lordec/lordec-releases/uploads/800a96d81b3348e368a0ff3a260a88e1/'] +sources = ['lordec-src_%(version)s.tar.bz2'] +patches = [ + 'LoRDEC-0.9_GATB.patch', + 'LoRDEC-0.9_GraphVector.patch', +] +checksums = [ + {'lordec-src_0.9.tar.bz2': '8108b82a8404fbf44c7e300d3abb43358ccc28993f90546168a20ca82536923b'}, + {'LoRDEC-0.9_GATB.patch': '8ff5e097455bb6ea515423bc76059f64d1983eb4873e640cd5021f00be85ca99'}, + {'LoRDEC-0.9_GraphVector.patch': '8c42dda643f8e1f79ee7d4ea2e3d8904cb755dc44cb907ada35b1e2873605ae5'}, +] + +local_gatb_version = '1.4.2' +dependencies = [ + ('Boost', '1.79.0'), + ('GATB-Core', local_gatb_version), +] + +build_cmd_targets = 'lordec_%s' % ''.join(local_gatb_version.split('.')) + +buildopts = "AUTOMATIC_LIBBOOST_LOCAL_INSTALL=no GATB=${EBROOTGATBMINCORE}" + +local_bins = ['lordec-%s' % x for x in ('build-SR-graph', 'correct', 'stat', 'trim', 'trim-split')] + +files_to_copy = [(local_bins, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [], +} + +sanity_check_commands = ["%s --help 2>&1 | grep 'using GATB v%s'" % (x, local_gatb_version) for x in local_bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GATB.patch b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GATB.patch new file mode 100644 index 000000000000..11304be190c5 --- /dev/null +++ b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GATB.patch @@ -0,0 +1,13 @@ +don't hardcode path to include/gatb/gatb_core.hpp so we can use GATB-Core provided as dependency +author: Kenneth Hoste (HPC-UGent) +--- lordec-src_0.9/Makefile.orig 2023-03-31 09:54:40.838204432 +0200 ++++ lordec-src_0.9/Makefile 2023-03-31 09:55:42.987061551 +0200 +@@ -63,7 +63,7 @@ + $(PROG_GRAPH) $(OBJS_TEST_CORRECT) $(OBJS_CATCHTEST_CORRECT) $(OBJS_CORRECT) $(OBJS_STATS) $(OBJS_TRIM) $(OBJS_TRIM_SPLIT): boost_include/boost/graph/graph_traits.hpp + endif + # ANYWAY we need GATB (compiled and installed) to compile all the objects +-$(PROG_GRAPH) $(OBJS_TEST_CORRECT) $(OBJS_CATCHTEST_CORRECT) $(OBJS_CORRECT) $(OBJS_STATS) $(OBJS_TRIM) $(OBJS_TRIM_SPLIT): gatb_v$(GATBVERSION)$(SUFFIX)/include/gatb/gatb_core.hpp ++$(PROG_GRAPH) $(OBJS_TEST_CORRECT) $(OBJS_CATCHTEST_CORRECT) $(OBJS_CORRECT) $(OBJS_STATS) $(OBJS_TRIM) $(OBJS_TRIM_SPLIT): $(GATB)/include/gatb/gatb_core.hpp + + # get version from a file + VERSION := $(shell cat version.txt) diff --git a/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch new file mode 100644 index 000000000000..da7be67c7df0 --- /dev/null +++ b/easybuild/easyconfigs/l/LoRDEC/LoRDEC-0.9_GraphVector.patch @@ -0,0 +1,75 @@ +port LoRDEC 0.9 to gatb-core >= 1.3.0 by replacing Graph::Vector to GraphVector +author: Kenneth Hoste (HPC-UGent) +diff -ru lordec-src_0.9.orig/lordec-correct.h lordec-src_0.9/lordec-correct.h +--- lordec-src_0.9.orig/lordec-correct.h 2018-06-04 15:44:49.000000000 +0200 ++++ lordec-src_0.9/lordec-correct.h 2023-03-31 22:17:39.105922332 +0200 +@@ -160,11 +160,11 @@ + // store the neighbors of begin node in the stack + + #if defined(GATB_V110) +- Graph::Vector neighbors = graph.successors(begin); ++ GraphVector neighbors = graph.successors(begin); + #elif defined(GATB_V130) || defined(GATB_V140) || defined(GATB_V141) + GraphVector neighbors = graph.successorsEdge(begin); + #else +- Graph::Vector neighbors = graph.successorsEdge(begin); ++ GraphVector neighbors = graph.successorsEdge(begin); + #endif + + // if (neighbors.size() == 1) +@@ -221,11 +221,11 @@ + } + } + #if defined(GATB_V110) +- Graph::Vector neighbors = graph.successors(cnode); ++ GraphVector neighbors = graph.successors(cnode); + #elif defined(GATB_V130) || defined(GATB_V140) || defined(GATB_V141) + GraphVector neighbors = graph.successorsEdge(cnode); + #else +- Graph::Vector neighbors = graph.successorsEdge(cnode); ++ GraphVector neighbors = graph.successorsEdge(cnode); + #endif + + // if (neighbors.size() == 1) +@@ -328,11 +328,11 @@ + + // store the neighbors of begin node in the stack + #if defined(GATB_V110) +- Graph::Vector neighbors = graph.successors(begin); ++ GraphVector neighbors = graph.successors(begin); + #elif defined(GATB_V130) || defined(GATB_V140) || defined(GATB_V141) + GraphVector neighbors = graph.successorsEdge(begin); + #else +- Graph::Vector neighbors = graph.successorsEdge(begin); ++ GraphVector neighbors = graph.successorsEdge(begin); + #endif + for (i = neighbors.size()-1; i>= 0; i--) { + nodes.push(new stack_element(neighbors[i].to, 1, ascii(neighbors[i].nt))); +@@ -396,11 +396,11 @@ + else { + + #if defined(GATB_V110) +- Graph::Vector neighbors = graph.successors(cnode); ++ GraphVector neighbors = graph.successors(cnode); + #elif defined(GATB_V130) || defined(GATB_V140) || defined(GATB_V141) + GraphVector neighbors = graph.successorsEdge(cnode); + #else +- Graph::Vector neighbors = graph.successorsEdge(cnode); ++ GraphVector neighbors = graph.successorsEdge(cnode); + #endif + for(i=neighbors.size()-1; i>=0; i--) { + Edge e = neighbors[i]; +@@ -450,11 +450,11 @@ + + while (true) { + #if defined(GATB_V110) +- Graph::Vector neighbors = graph.successors(node); ++ GraphVector neighbors = graph.successors(node); + #elif defined(GATB_V130) || defined(GATB_V140) || defined(GATB_V141) + GraphVector neighbors = graph.successorsEdge(node); + #else +- Graph::Vector neighbors = graph.successorsEdge(node); ++ GraphVector neighbors = graph.successorsEdge(node); + #endif + if (neighbors.size() == 0) // dead end + return DEADEND; diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb index d1e9278c0bf0..c11baed27971 100644 --- a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.5-GCCcore-11.3.0.eb @@ -1,8 +1,4 @@ -# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. -# Updated to 0.4.3 and GCCcore-10.2.0 -# J. Sassmannshausen (GSTT/NHS UK) -# -easyblock = 'Binary' +easyblock = 'Cargo' name = 'Longshot' version = '0.4.5' @@ -15,26 +11,322 @@ description = """Longshot is a variant calling tool for diploid genomes using lo toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -github_account = 'pjedge' -source_urls = [GITHUB_SOURCE] +crates = [ + ('addr2line', '0.19.0'), + ('adler', '1.0.2'), + ('ahash', '0.7.6'), + ('aho-corasick', '0.7.20'), + ('android_system_properties', '0.1.5'), + ('ansi_term', '0.12.1'), + ('approx', '0.3.2'), + ('atty', '0.2.14'), + ('autocfg', '1.1.0'), + ('backtrace', '0.3.67'), + ('bio', '0.25.0'), + ('bio-types', '0.13.0'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '1.3.2'), + ('bumpalo', '3.12.0'), + ('bv', '0.10.0'), + ('bytecount', '0.3.2'), + ('byteorder', '1.4.3'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.0.79'), + ('cfg-if', '1.0.0'), + ('chrono', '0.4.24'), + ('clap', '2.34.0'), + ('cmake', '0.1.50'), + ('codespan-reporting', '0.11.1'), + ('core-foundation-sys', '0.8.3'), + ('csv', '1.2.1'), + ('csv-core', '0.1.10'), + ('curl-sys', '0.4.61+curl-8.0.1'), + ('custom_derive', '0.1.7'), + ('cxx', '1.0.94'), + ('cxx-build', '1.0.94'), + ('cxxbridge-flags', '1.0.94'), + ('cxxbridge-macro', '1.0.94'), + ('derive-new', '0.5.9'), + ('either', '1.8.1'), + ('error-chain', '0.12.4'), + ('feature-probe', '0.1.1'), + ('fishers_exact', '1.0.1'), + ('fnv', '1.0.7'), + ('form_urlencoded', '1.1.0'), + ('fs-utils', '1.1.4'), + ('fuchsia-cprng', '0.1.1'), + ('fxhash', '0.2.1'), + ('getrandom', '0.2.8'), + ('gimli', '0.27.2'), + ('glob', '0.3.1'), + ('hashbrown', '0.11.2'), + ('heck', '0.4.1'), + ('hermit-abi', '0.1.19'), + ('hts-sys', '2.0.3'), + ('iana-time-zone', '0.1.54'), + ('iana-time-zone-haiku', '0.1.1'), + ('idna', '0.3.0'), + ('ieee754', '0.2.6'), + ('itertools', '0.7.11'), + ('itertools-num', '0.1.3'), + ('itoa', '1.0.6'), + ('jobserver', '0.1.26'), + ('js-sys', '0.3.61'), + ('lazy_static', '1.4.0'), + ('libc', 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'8e5180c00cd44c9b1c88adb3693291f1cd93605ded80c250a75d472756b4d071'}, + {'windows_aarch64_gnullvm-0.42.2.tar.gz': '597a5118570b68bc08d8d59125332c54f1ba9d9adeedeef5b99b02ba2b0698f8'}, + {'windows_aarch64_msvc-0.42.2.tar.gz': 'e08e8864a60f06ef0d0ff4ba04124db8b0fb3be5776a5cd47641e942e58c4d43'}, + {'windows_i686_gnu-0.42.2.tar.gz': 'c61d927d8da41da96a81f029489353e68739737d3beca43145c8afec9a31a84f'}, + {'windows_i686_msvc-0.42.2.tar.gz': '44d840b6ec649f480a41c8d80f9c65108b92d89345dd94027bfe06ac444d1060'}, + {'windows_x86_64_gnu-0.42.2.tar.gz': '8de912b8b8feb55c064867cf047dda097f92d51efad5b491dfb98f6bbb70cb36'}, + {'windows_x86_64_gnullvm-0.42.2.tar.gz': '26d41b46a36d453748aedef1486d5c7a85db22e56aff34643984ea85514e94a3'}, + {'windows_x86_64_msvc-0.42.2.tar.gz': '9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0'}, +] builddependencies = [ ('binutils', '2.38'), ('Rust', '1.65.0'), ('Clang', '13.0.1'), - ('CMake', '3.23.1'), + ('Perl', '5.34.1'), + ('CMake', '3.24.3'), ] dependencies = [ ('bzip2', '1.0.8'), ] -extract_sources = True - -install_cmd = "cargo install --root %(installdir)s --path ." - sanity_check_paths = { 'files': ['bin/%(namelower)s'], 'dirs': [], diff --git a/easybuild/easyconfigs/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..5ebb3d807a45 --- /dev/null +++ b/easybuild/easyconfigs/l/libGDSII/libGDSII-0.21-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libGDSII' +version = '0.21' + +homepage = 'https://github.com/HomerReid/libGDSII' +description = """libGDSII is a C++ library for working with GDSII binary data files, + intended primarily for use with the computational electromagnetism codes + scuff-em and meep but sufficiently general-purpose to allow other uses as well.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/HomerReid/libGDSII/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['31c90a4fb699746d051c0c597ef0543889c9f17b2a711fed398756ac4f1b1f4c'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/GDSIIConvert', 'include/libGDSII.h', 'lib/libGDSII.a', 'lib/libGDSII.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb new file mode 100644 index 000000000000..acb270672178 --- /dev/null +++ b/easybuild/easyconfigs/l/libGridXC/libGridXC-1.1.0-gompi-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'libGridXC' +version = '1.1.0' + +homepage = 'https://gitlab.com/siesta-project/libraries/libgridxc' +description = """A library to compute the exchange and correlation energy + and potential in spherical (i.e. atoms) or periodic systems.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True, 'opt': True} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libgridxc/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e7883e57a4db2438ee59437740291c06e0cfe1c8ae1901e4001f32312307e46a'] + +configopts = "-DWITH_MPI=ON -DWITH_LIBXC=ON" + +preconfigopts = 'CPATH= ' # gfortran ignores CPATH, but pkgconf also excludes dirs from CPATH + +dependencies = [('libxc', '5.2.3')] + +builddependencies = [ + ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), +] + +sanity_check_paths = { + 'files': ['lib/libgridxc.a'], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/libgridxc'], +} + +runtest = 'test' + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb new file mode 100644 index 000000000000..3b6c72c06b56 --- /dev/null +++ b/easybuild/easyconfigs/l/libPSML/libPSML-1.1.12-GCC-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'libPSML' +version = '1.1.12' + +homepage = 'https://gitlab.com/siesta-project/libraries/libpsml' +description = """A library to handle pseudopotentials in PSML format""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libpsml/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c61503d5a5de119f970f1bf27aa0ac8059b87e81d1a8013bef1bb7993df44c56'] + +dependencies = [ + ('xmlf90', '1.5.6'), +] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['lib/libpsml.a'], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/libpsml'], +} + +runtest = 'test' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..b8e5a2762f5e --- /dev/null +++ b/easybuild/easyconfigs/l/libRmath/libRmath-4.2.1-GCCcore-11.3.0.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# Updated: Denis Kristak (INUITS) +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'libRmath' +version = '4.2.1' + +homepage = 'https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-standalone-Rmath-library' +description = """The routines supporting the distribution and special functions in R and a few others are declared + in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = ['R-%(version)s.tar.gz'] +checksums = ['4d52db486d27848e54613d4ee977ad952ec08ce17807e1b525b10cd4436c643f'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('cURL', '7.83.0'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('zlib', '1.2.12'), + ('PCRE2', '10.40'), +] + +preconfigopts = "cd %(builddir)s/R-%(version)s && " +configopts = "--with-readline=no --with-recommended-packages=no --with-x=no" + +parallel = 1 + +postinstallcmds = ['cp -r %(builddir)s/R-%(version)s/src/include/R_ext %(installdir)s/include/'] +runtest = 'check' +start_dir = 'src/nmath/standalone' + +sanity_check_paths = { + 'files': ['lib/libRmath.%s' % SHLIB_EXT, 'lib/%(name)s.a', 'lib/pkgconfig/%(name)s.pc', 'include/Rmath.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb new file mode 100644 index 000000000000..41c152957ce4 --- /dev/null +++ b/easybuild/easyconfigs/l/libWallModelledLES/libWallModelledLES-0.6.1-foss-2021b.eb @@ -0,0 +1,46 @@ +name = "libWallModelledLES" +version = "0.6.1" +easyblock = "Binary" + +homepage = "https://bitbucket.org/lesituu/libwallmodelledles/" +description = """libWallModelledLES is a library based on OpenFOAM® technology, +extending the capabilities of OpenFOAM in the area of wall-modelled LES (WMLES). +This is a turbulence modelling methodology, which allows to make LES cheaper +by not resolving the inner region of turbulent boundary layers.""" + +toolchain = {"name": "foss", "version": "2021b"} +# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. +# Disabling vectorize was confirmed to fix the the known issues. +# With no test suite, sticking to known working toolchain options until proven otherwise. +toolchainopts = {"cstd": "c++11", "vectorize": False} + +source_urls = ["https://bitbucket.org/lesituu/libwallmodelledles/get/"] +sources = ["v%(version)s.tar.gz"] +checksums = ["06b2c06ef76b5247c0a0c0260ea1e4a58bed8e930d0a0add9fe60e626c4bc0f8"] + +dependencies = [ + ("OpenFOAM", "v2112"), +] + +extract_sources = True + +install_cmd = "source $FOAM_BASH && " + +# variables of target install directory +install_cmd += "export WM_PROJECT_USER_DIR=%(installdir)s && " +install_cmd += "export FOAM_USER_APPBIN=%(installdir)s/bin && " +install_cmd += "export FOAM_USER_LIBBIN=%(installdir)s/lib && " +install_cmd += "export LD_LIBRARY_PATH=%(installdir)s/lib:$LD_LIBRARY_PATH && " + +install_cmd += "pwd && ls && ./Allwmake -j %(parallel)s " +install_cmd += " && cp -av tests %(installdir)s " + +sanity_check_paths = { + "files": ["lib/libWallModelledLES.%s" % SHLIB_EXT], + "dirs": ["tests"], +} +sanity_check_commands = [ + "source $FOAM_BASH && cd %(installdir)s/tests/testCases/channel_flow && pimpleFoam" +] + +moduleclass = "cae" diff --git a/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..64d50b5219dc --- /dev/null +++ b/easybuild/easyconfigs/l/libaio/libaio-0.3.113-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'libaio' +version = '0.3.113' +_libversion = '1.0.2' + +homepage = 'https://pagure.io/libaio' +description = "Asynchronous input/output library that uses the kernels native interface." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://pagure.io/%(name)s/archive/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['1c561c20670c5c09cc8437a622008c0693c6a7816c1f30332da3796953b2f454'] + +builddependencies = [('binutils', '2.39')] + +_soname = "libaio.%s.%s" % (SHLIB_EXT, _libversion) + +files_to_copy = [ + (["src/libaio.a", "src/%s" % _soname], "lib"), + (["src/libaio.h"], "include"), +] + +# links to the shared library with generic names +_solinks = [ + "libaio.%s" % SHLIB_EXT, + "libaio.%s.1" % SHLIB_EXT, +] + +postinstallcmds = ["cd %%(installdir)s/lib && ln -s %s %s" % (_soname, l) for l in _solinks] + +sanity_check_paths = { + 'files': ['lib/%s' % l for l in ['libaio.a', _soname] + _solinks] + ['include/libaio.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..3126faae1c50 --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libarchive' +version = '3.6.2' + +homepage = 'https://www.libarchive.org/' + +description = """ + Multi-format archive and compression library +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://www.libarchive.org/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ba6d02f15ba04aba9c23fd5f236bb234eab9d5209e95d1c4df85c44d5f19b9b3'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('XZ', '5.4.2'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-13.1.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..f0260cb95ae6 --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-13.1.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libarchive' +version = '3.6.2' + +homepage = 'https://www.libarchive.org/' + +description = """ + Multi-format archive and compression library +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = ['https://www.libarchive.org/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ba6d02f15ba04aba9c23fd5f236bb234eab9d5209e95d1c4df85c44d5f19b9b3'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('XZ', '5.4.2'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..3dfc9fe295bd --- /dev/null +++ b/easybuild/easyconfigs/l/libctl/libctl-4.5.1-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libctl' +version = '4.5.1' + +homepage = 'https://libctl.readthedocs.io/en/latest/' +description = """libctl is a free Guile-based library implementing flexible control files for scientific simulations.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/NanoComp/libctl/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['fcfeb2f13dda05b560f0ec6872757d9318fdfe8f4bc587eb2053a29ba328ae25'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), # required for libtool +] + +dependencies = [('Guile', '3.0.9')] + +configopts = '--with-pic --enable-shared' + +sanity_check_paths = { + 'files': ['bin/gen-ctl-io', 'lib/libctl.a', 'lib/libctlgeom.a', + 'lib/libctlgeom.%s' % SHLIB_EXT, 'lib/libctl.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.18-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.18-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..3e44ca69301d --- /dev/null +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.18-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeMake' + +name = 'libdeflate' +version = '1.18' + +homepage = 'https://github.com/ebiggers/libdeflate' +description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'ebiggers' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['225d982bcaf553221c76726358d2ea139bb34913180b20823c782cede060affd'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', + 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'include/%(name)s.h', + ], + 'dirs': [], +} +sanity_check_commands = [ + '%(name)s-gzip -h', + '%(name)s-gunzip -h', +] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..61bf17145f59 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.12' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..416e39457062 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.4.4' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libffi/libffi/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d66c56ad259a82cf2a9dfc408b32bf5da52371500b84745f7fb8b645712df676'] + +builddependencies = [ + ('binutils', '2.40'), +] + +configopts = '--disable-exec-static-tramp ' + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-13.1.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..d64748fec2e3 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-13.1.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.4.4' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libffi/libffi/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d66c56ad259a82cf2a9dfc408b32bf5da52371500b84745f7fb8b645712df676'] + +builddependencies = [ + ('binutils', '2.40'), +] + +configopts = '--disable-exec-static-tramp ' + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..cb07437830e7 --- /dev/null +++ b/easybuild/easyconfigs/l/libgcrypt/libgcrypt-1.10.1-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libgcrypt' +version = '1.10.1' + +homepage = 'https://gnupg.org/related_software/libgcrypt/index.html' +description = """Libgcrypt is a general purpose cryptographic library originally based on code from GnuPG""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['ef14ae546b0084cd84259f61a55e07a38c3b53afc0f546bffcef2f01baffe9de'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('libgpg-error', '1.46')] + +sanity_check_paths = { + 'files': ['bin/libgcrypt-config', 'include/gcrypt.h', 'lib/libgcrypt.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +sanity_check_commands = [ + 'dumpsexp --version', + 'hmac256 --version', + 'mpicalc --version', + 'libgcrypt-config --version | grep "%(version)s"', +] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..f11da8ce8493 --- /dev/null +++ b/easybuild/easyconfigs/l/libgeotiff/libgeotiff-1.7.1-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libgeotiff' +version = '1.7.1' + +homepage = 'https://directory.fsf.org/wiki/Libgeotiff' +description = """Library for reading and writing coordinate system information from/to GeoTIFF files""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.osgeo.org/geotiff/libgeotiff'] +sources = [SOURCE_TAR_GZ] +checksums = ['05ab1347aaa471fc97347d8d4269ff0c00f30fa666d956baba37948ec87e55d6'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('PROJ', '9.2.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('zlib', '1.2.13'), + ('SQLite', '3.42.0'), + ('LibTIFF', '4.5.0'), + ('cURL', '8.0.1'), +] + +configopts = ' --with-libtiff=$EBROOTLIBTIFF --with-proj=$EBROOTPROJ --with-zlib=$EBROOTZLIB' +configopts += ' --with-jpeg=$EBROOTLIBJPEGMINTURBO' + +sanity_check_paths = { + 'files': ['bin/listgeo', 'lib/libgeotiff.a', 'lib/libgeotiff.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..7b7f71ea537c --- /dev/null +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'libharu' +version = '2.3.0' + +homepage = 'https://github.com/libharu/libharu/' +description = """libHaru is a free, cross platform, open source library for generating PDF files.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GITHUB_SOURCE] # https://github.com/libharu/libharu/archive/ +sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['8f9e68cc5d5f7d53d1bc61a1ed876add1faf4f91070dbc360d8b259f46d9a4d2'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [('libpng', '1.6.37')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libhpdf.%s' % SHLIB_EXT], + 'dirs': [ + 'if', + 'include', + 'lib', + ] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..2f013448152e --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.3.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libiconv' +version = '1.17' + +homepage = 'https://www.gnu.org/software/libiconv' +description = "Libiconv converts from one character encoding to another through Unicode conversion" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['8f74213b56238c85a50a5329f77e06198771e70dd9a739779f4c02f65d971313'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', + 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.5.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..db21ae7cbeb0 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.5.1-GCCcore-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'libjpeg-turbo' +version = '2.1.5.1' + +homepage = 'https://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2fdc3feb6e9deb17adec9bafa3321419aa19f8f4e5dea7bf8486844ca22207bf'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +dependencies = [ + ('NASM', '2.16.01'), +] + +configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmaus2/libmaus2-2.0.499-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libmaus2/libmaus2-2.0.499-GCC-11.3.0.eb new file mode 100644 index 000000000000..5aa65b14cf19 --- /dev/null +++ b/easybuild/easyconfigs/l/libmaus2/libmaus2-2.0.499-GCC-11.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libmaus2' +version = '2.0.499' + +homepage = 'https://github.com/gt1/libmaus2' +description = "libmaus2 is a collection of data structures and algorithms." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/gt1/libmaus2/archive/'] +sources = ['%(version)s-release-20180606122508.tar.gz'] +checksums = ['5e3643bb14a3342b76b68592252f248e5e97725caffe6a6a3274563a0433338a'] + +sanity_check_paths = { + 'files': ['lib/libmaus2.a', 'lib/libmaus2.%s' % SHLIB_EXT, + 'lib/libmaus2_simd_align_128.a', 'lib/libmaus2_simd_align_128.%s' % SHLIB_EXT, + 'lib/libmaus2_simd_align_256.a', 'lib/libmaus2_simd_align_256.%s' % SHLIB_EXT], + 'dirs': ['include/libmaus2'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..8d57716f577e --- /dev/null +++ b/easybuild/easyconfigs/l/libogg/libogg-1.3.5-GCCcore-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libogg' +version = '1.3.5' + +homepage = 'https://xiph.org/ogg/' +description = """Ogg is a multimedia container format, and the native file and stream format for the Xiph.org +multimedia codecs.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/ogg/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c4d91be36fc8e54deae7575241e03f4211eb102afb3fc0775fbbc1b740016705'] + +builddependencies = [('binutils', '2.40')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libogg.a', 'lib/libogg.%s' % SHLIB_EXT], + 'dirs': ['include/ogg'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libopus/libopus-1.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libopus/libopus-1.4-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..576b4556eec0 --- /dev/null +++ b/easybuild/easyconfigs/l/libopus/libopus-1.4-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libopus' +version = '1.4' + +homepage = 'https://www.opus-codec.org/' +description = """Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive + speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is + standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s + SILK codec and Xiph.Org’s CELT codec.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://downloads.xiph.org/releases/opus/'] +sources = ['opus-%(version)s.tar.gz'] +checksums = ['c9b32b4253be5ae63d1ff16eea06b94b5f0f2951b7a02aceef58e3a3ce49c51f'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libopus.a', 'lib/libopus.%s' % SHLIB_EXT], + 'dirs': ['include/opus'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.39-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.39-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..1bd630a9c13b --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.39-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.39' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' + +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['af4fb7f260f839919e5958e5ab01a275d4fe436d45442a36ee62f73e5beb75ba'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('zlib', '1.2.13')] + +local_majminver = '%(version_major)s%(version_minor)s' + +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', + 'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT, + 'lib/libpng%s.a' % local_majminver, + 'lib/libpng%s.%s' % (local_majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % local_majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..ade8ec67a130 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.2' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['3feb7171f16a84ee82ca18a36d7b9be109a52c04f492a053331d7d1095007c35'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('ncurses', '6.4'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.1.0.eb b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..2c0323f20bf0 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-8.2-GCCcore-13.1.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libreadline' +version = '8.2' + +homepage = 'https://tiswww.case.edu/php/chet/readline/rltop.html' +description = """ + The GNU Readline library provides a set of functions for use by applications + that allow users to edit command lines as they are typed in. Both Emacs and + vi editing modes are available. The Readline library includes additional + functions to maintain a list of previously-entered command lines, to recall + and perhaps reedit those lines, and perform csh-like history expansion on + previous commands. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/readline'] +sources = ['readline-%(version)s.tar.gz'] +checksums = ['3feb7171f16a84ee82ca18a36d7b9be109a52c04f492a053331d7d1095007c35'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('ncurses', '6.4'), +] + +# for the termcap symbols, use EB ncurses +buildopts = "SHLIB_LIBS='-lncurses'" + +sanity_check_paths = { + 'files': ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x + for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', + 'rlconf.h', 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..2547b2017647 --- /dev/null +++ b/easybuild/easyconfigs/l/libsigc++/libsigc++-3.4.0-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +# Updated to CMakeMake +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'libsigc++' +version = '3.4.0' + +homepage = 'https://libsigcplusplus.github.io/libsigcplusplus/' +description = """The libsigc++ package implements a typesafe callback system +for standard C++.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['02e2630ffb5ce93cd52c38423521dfe7063328863a6e96d41d765a6116b8707e'] + +builddependencies = [ + ('binutils', '2.38'), + ('Graphviz', '5.0.0'), + ('libxslt', '1.1.34'), + ('mm-common', '1.0.5'), + ('CMake', '3.24.3'), +] + +test_cmd = 'ctest' +runtest = '-j' + +sanity_check_paths = { + 'files': ['lib/libsigc-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..0535f0e96f82 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'libspatialindex' +version = '1.9.3' + +homepage = 'https://libspatialindex.org' +description = """C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/libspatialindex/libspatialindex/releases/download/%(version)s/'] +sources = ['spatialindex-src-%(version)s.tar.gz'] +checksums = ['47d8779e32477b330e46b62fb7e62cb812caee5d8e684c35cb635a42a749f3fc'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['lib/libspatialindex.%s' % SHLIB_EXT], + 'dirs': ['include/spatialindex'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.3-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..409cc8bc2a02 --- /dev/null +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.3-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libtirpc' +version = '1.3.3' + +homepage = 'https://sourceforge.net/projects/libtirpc/' +description = "Libtirpc is a port of Suns Transport-Independent RPC library to Linux." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['6474e98851d9f6f33871957ddee9714fdcd9d8a5ee9abb5a98d63ea2e60e12f3'] + +configopts = '--enable-static --enable-shared --disable-gssapi' + +builddependencies = [ + ('binutils', '2.40') +] + +sanity_check_paths = { + 'files': ['lib/libtirpc.%s' % (x,) for x in ['a', SHLIB_EXT]], + 'dirs': ['include/tirpc', 'lib'], +} + +modextrapaths = {'CPATH': 'include/tirpc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..d3c279ea3437 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.7-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.7' + +homepage = 'https://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['04e96c2404ea70c590c546eba4202a4e12722c640016c12b9b2f1ce3d481e9a8'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('M4', '1.4.19'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..f93fd922791e --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-1.1-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '1.1' + +homepage = 'https://www.gnu.org/software/libunistring/' + +description = """This library provides functions for manipulating Unicode strings and for + manipulating C strings according to the Unicode standard.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['827c1eb9cb6e7c738b171745dac0888aa58c5924df2e59239318383de0729b98'] + +builddependencies = [ + ('binutils', '2.35'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..9ca69508042b --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.6.2' + +homepage = 'https://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4a6aec666991fb45d0889c44aede8ad6eb108071c3554fcdff671f9c94794976'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('XZ', '5.4.2'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fno-common" && ' + +sanity_check_paths = { + 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..40c5f137808e --- /dev/null +++ b/easybuild/easyconfigs/l/libvorbis/libvorbis-1.3.7-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libvorbis' +version = '1.3.7' + +homepage = 'https://xiph.org/vorbis/' +description = """Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed +audio format""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.osuosl.org/pub/xiph/releases/vorbis/'] +sources = [SOURCE_TAR_XZ] +checksums = ['b33cc4934322bcbf6efcbacf49e3ca01aadbea4114ec9589d1b1e9d20f72954b'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [('libogg', '1.3.5')] + +configopts = '--enable-static --enable-shared' + +sanity_check_paths = { + 'files': ['lib/libvorbis.a', 'lib/libvorbis.%s' % SHLIB_EXT], + 'dirs': ['include/vorbis'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb new file mode 100644 index 000000000000..4549d2c41b2c --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '6.1.0' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a3aa16915942543031a5d9c4a92c439ce54249bdcda8c91c4e69e65329dc9a54'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Perl', '5.36.0'), +] + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'], +} + +sanity_check_commands = ['xc-info 1'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb new file mode 100644 index 000000000000..8973869bc362 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '6.1.0' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a3aa16915942543031a5d9c4a92c439ce54249bdcda8c91c4e69e65329dc9a54'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Perl', '5.36.0'), +] + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_FORTRAN03=ON -DENABLE_XHOST=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +parallel = 1 + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'], +} + +sanity_check_commands = ['xc-info 1'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.11.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.11.4-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..13845741e033 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.11.4-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.11.4' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['737e1d7f8ab3f139729ca13a2494fd17bf30ddb4b7a427cf336252cab57f57f7'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..171353e0fac8 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.38-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.38' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.gnome.org/sources/libxslt/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['1f32450425819a09acaff2ab7a5a7f8a2ec7956e505d7beeb45e843d0e1ecab1'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('libxml2', '2.11.4'), +] + +# Make sure it doesn't pick up OS installed libgcrypt or Python +configopts = '--with-crypto=no --with-python=no ' + +sanity_check_paths = { + 'files': ['bin/xsltproc', 'include/libxslt/xslt.h', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb new file mode 100644 index 000000000000..9fbbdba63298 --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.17' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/hfp/libxsmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8b642127880e92e8a75400125307724635ecdf4020ca4481e5efe7640451bb92'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..76fee75bd36d --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.2.5' + +homepage = 'https://pyyaml.org/wiki/LibYAML' +description = "LibYAML is a YAML parser and emitter written in C." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://pyyaml.org/download/%(name)s/'] +sources = ['yaml-%(version)s.tar.gz'] +checksums = ['c642ae9b75fee120b2d96c712538bd2cf283228d2337df2cf2988e3c02678ef4'] + +builddependencies = [ + ('binutils', '2.40'), +] + + +sanity_check_paths = { + 'files': ['include/yaml.h', 'lib/libyaml.a', 'lib/libyaml.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lifelines/lifelines-0.27.4-foss-2022a.eb b/easybuild/easyconfigs/l/lifelines/lifelines-0.27.4-foss-2022a.eb new file mode 100644 index 000000000000..c300ce4d3a6f --- /dev/null +++ b/easybuild/easyconfigs/l/lifelines/lifelines-0.27.4-foss-2022a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'lifelines' +version = '0.27.4' + +homepage = "https://lifelines.readthedocs.io/en/latest/" +description = """lifelines is a complete survival analysis library, written in pure Python.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('interface_meta', '1.3.0', { + 'checksums': ['8a4493f8bdb73fb9655dcd5115bc897e207319e36c8835f39c516a2d7e9d79a1'], + }), + ('autograd', '1.5', { + 'checksums': ['d80bd225154d1db13cb4eaccf7a18c358be72092641b68717f96fcf1d16acd0b'], + }), + ('autograd-gamma', '0.5.0', { + 'checksums': ['f27abb7b8bb9cffc8badcbf59f3fe44a9db39e124ecacf1992b6d952934ac9c4'], + }), + ('formulaic', '0.4.0', { + 'checksums': ['087950518c53a2491deb52b8ddd66833f953882e517a42e476c007cc8f6892c5'], + }), + (name, version, { + 'checksums': ['62f7e911a64c8f723eef4207174fb1df39a94f79eca557cdf53d310eb6be132f'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2022a.eb b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2022a.eb new file mode 100644 index 000000000000..a718a90a2431 --- /dev/null +++ b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2022a.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'loompy' +version = '3.0.7' + +homepage = 'https://loompy.org/' +description = "Python implementation of the Loom file format, an efficient file format for large omics datasets" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), + ('numba', '0.56.4'), +] + +use_pip = True + +exts_list = [ + ('numpy-groupies', '0.9.20', { + 'sources': ['numpy_groupies-%(version)s.tar.gz'], + 'checksums': ['923a382d6bc6876384b58a9c0503b05b9d36a660f329695c2d33e4f93fcbbe3d'], + }), + (name, version, { + 'checksums': ['b5cdf7b54734c6bed3a181d11947af70af2c6e0dcadc02fd0e871df232faa8f4'], + }), +] + +sanity_check_paths = { + 'files': ['bin/loompy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["loompy --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/lxml/lxml-4.9.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/lxml/lxml-4.9.2-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..20323870198f --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-4.9.2-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '4.9.2' + +homepage = 'https://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2455cfaeb7ac70338b3257f41e21f0724f4b5b0c0e7702da67ee6c3640835b67'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('libxml2', '2.10.3'), + ('libxslt', '1.1.37'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..1386e6dc6155 --- /dev/null +++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'lz4' +version = '1.9.4' + +homepage = 'https://lz4.github.io/lz4/' +description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. + It features an extremely fast decoder, with speed in multiple GB/s per core.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['0b0e3aa07c8c063ddf40b082bdf7e37a1562bda40a0ff5272957f3e987e0e54b'] + +builddependencies = [('binutils', '2.40')] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M3GNet/M3GNet-0.2.4-foss-2022a.eb b/easybuild/easyconfigs/m/M3GNet/M3GNet-0.2.4-foss-2022a.eb new file mode 100644 index 000000000000..65f7885f2069 --- /dev/null +++ b/easybuild/easyconfigs/m/M3GNet/M3GNet-0.2.4-foss-2022a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'M3GNet' +version = '0.2.4' + +homepage = 'https://materialsvirtuallab.github.io/m3gnet/' +description = """" +M3GNet is a new materials graph neural network architecture that incorporates +3-body interactions. A key difference with prior materials graph +implementations such as MEGNet is the addition of the coordinates for atoms and +the 3×3 lattice matrix in crystals, which are necessary for obtaining tensorial +quantities such as forces and stresses via auto-differentiation. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('ASE', '3.22.1'), + ('TensorFlow', '2.11.0'), + ('pymatgen', '2023.3.10'), + ('h5py', '3.7.0'), # optional, for model saving +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['a7f82b06f48d8fb81f91fb88484177005066cdf708902bf749afaa7f8d117ce8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/m3g'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/m3gnet'], +} + +sanity_check_commands = ['m3g --help'] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..9bed7ee958f5 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.40', '', SYSTEM)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..5f8b9df7e744 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.19-GCCcore-13.1.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.19' + +homepage = 'https://www.gnu.org/software/m4/m4.html' +description = """GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible + although it has some extensions (for example, handling more than 9 positional parameters to macros). + GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3be4a26d825ffdfda52a56fc43246456989a3630093cced3fbddf4771ee58a70'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.40', '', SYSTEM)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/easybuilders/easybuild-easyconfigs/issues/529 +configopts = "--enable-c++ CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ['bin/m4'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb new file mode 100644 index 000000000000..cc54713c3c69 --- /dev/null +++ b/easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2022a.eb @@ -0,0 +1,36 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +# Updated: Denis Kristak (Inuits) +easyblock = 'PythonPackage' + +name = 'MAGeCK' +version = '0.5.9.4' + +homepage = "https://sourceforge.net/p/mageck/wiki/Home/" +description = """Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify + important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology. MAGeCK is developed + by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Dana-Farber Cancer Institute, and is being actively updated + by Wei Li lab from Children's National Medical Center.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['42875b308f2d9ee38f083fb1020d7d48fca29e2100fdb09ced1969b738b8c939'] + +# Remove the shipped mageckGSEA and RRA binaries so that the Python install will build them +# This avoids RPATH problems (see #15082) +preinstallopts = "rm bin/{mageckGSEA,RRA} && " + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +sanity_check_commands = ["cd %(builddir)s/%(namelower)s-%(version)s/demo/demo1 && ./run.sh"] + [ + "%s -h" % x for x in ['mageck', 'mageckGSEA']] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb index 6a6d50726d58..4b61ca4d1d3f 100644 --- a/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MAKER/MAKER-3.01.04-foss-2022a.eb @@ -29,7 +29,7 @@ dependencies = [ exts_defaultclass = 'PerlModule' exts_filter = ("perldoc -lm %(ext_name)s ", "") -_libdir = 'lib/perl5/site_perl/%(perlver)s/' +_libdir = 'lib/perl5/site_perl/%(perlver)s' exts_list = [ ('Acme::Damn', '0.08', { @@ -74,9 +74,11 @@ exts_list = [ }), (name, version, { 'modulename': False, + # fix hardcoded paths to libraries + 'preinstallopts': r"find ../ -type f -exec sed -i 's|RealBin/\.\./lib|RealBin/../%s|g' {} \; && " % _libdir, 'postinstallcmds': [ 'cp -a ../bin %(installdir)s/', - 'cp -an blib/lib/* ../lib/* %%(installdir)s/%s' % _libdir, + 'cp -an blib/lib/* ../lib/* %%(installdir)s/%s/' % _libdir, ], 'source_tmpl': 'Version_%(version)s.tar.gz', 'source_urls': ['https://github.com/Yandell-Lab/maker/archive/refs/tags/'], diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2022b-r5.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2022b-r5.eb new file mode 100644 index 000000000000..4ffbc9807725 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2022b-r5.eb @@ -0,0 +1,28 @@ +name = 'MATLAB' +version = '2022b' +_update = '5' +versionsuffix = '-r%s' % _update + +homepage = 'https://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = SYSTEM + +sources = ['R%s_Update_%s_Linux.iso' % (version, _update)] +checksums = ['d11ba428a6970208f0855138a6e2253c31e2ead34d51da125529a208945ac187'] + +java_options = '-Xmx2048m' + +osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files + +# Use EB_MATLAB_KEY environment variable or uncomment and modify license key +# key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' + +# Use EB_MATLAB_LICENSE_SERVER and EB_MATLAB_LICENSE_SERVER_PORT environment variables or +# uncomment and modify the following variables for installation with floating license server +# license_file = 'my-license-file' +# license_server_port = 'XXXXX' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.4.2-foss-2021a.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.4.2-foss-2021a.eb new file mode 100644 index 000000000000..e5f35ff61b3c --- /dev/null +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.4.2-foss-2021a.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'MDAnalysis' +version = '2.4.2' + +homepage = 'https://www.mdanalysis.org/' +description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) +simulations in many popular formats.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('networkx', '2.5.1'), + ('tqdm', '4.61.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mrcfile', '1.4.3', { + 'checksums': ['43c358c59ff8f583fc4dc2079a0099028719109ebf92066e388772bab389c5f5'], + }), + ('GridDataFormats', '1.0.1', { + 'modulename': 'gridData', + 'checksums': ['ad2c9ab7d672a6d8c426de7d083eee4f3e2b0bd59391675d30683c768ab83cc4'], + }), + ('gsd', '2.8.0', { + 'checksums': ['f2b031a26a7a5bee5f3940dc2f36c5a5b6670307b297c526adf2e26c1f5b46ae'], + }), + ('msgpack', '1.0.5', { + 'checksums': ['c075544284eadc5cddc70f4757331d99dcbc16b2bbd4849d15f8aae4cf36d31c'], + }), + ('mmtf-python', '1.1.3', { + 'modulename': 'mmtf', + 'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'], + }), + ('fasteners', '0.18', { + 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], + }), + # MDAnalysis 2.4.x requires biopython >= 1.80 + ('biopython', '1.81', { + 'checksums': ['2cf38112b6d8415ad39d6a611988cd11fb5f33eb09346666a87263beba9614e0'], + 'runtest': "python setup.py test --offline", + 'modulename': 'Bio', + 'sanity_check_commands': ["python -c 'import Bio.MarkovModel'"], + }), + (name, version, { + 'modulename': 'MDAnalysis', + 'checksums': ['ae2ee5627391e73f74eaa3c547af3ec6ab8b040d27dedffe3a7ece8e0cd27636'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..2a363ae76ca9 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +name = 'METIS' +version = '5.1.0' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' + +description = """ + METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s-use-doubles.patch'] +checksums = [ + {'metis-5.1.0.tar.gz': '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2'}, + {'METIS-5.1.0-use-doubles.patch': '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67'}, +] + +# We use 32bit for indices and 64bit for content +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MOABB/MOABB-0.4.6-foss-2021a.eb b/easybuild/easyconfigs/m/MOABB/MOABB-0.4.6-foss-2021a.eb new file mode 100644 index 000000000000..dffd885177d4 --- /dev/null +++ b/easybuild/easyconfigs/m/MOABB/MOABB-0.4.6-foss-2021a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'MOABB' +version = '0.4.6' + +homepage = 'https://neurotechx.github.io/moabb/' +description = """Build a comprehensive benchmark of popular Brain-Computer Interface (BCI) +algorithms applied on an extensive list of freely available EEG datasets.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('MNE-Python', '0.24.1'), + ('h5py', '3.2.1'), + ('scikit-learn', '0.24.2'), + ('matplotlib', '3.4.2'), + ('Seaborn', '0.11.2'), + ('PyYAML', '5.4.1'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +# relax requirements of unmatchable dependencies (requirements seem quite arbitrary) +_relax_req = ';'.join(['s/^%s.*/%s = "*"/' % (d, d) for d in ['scikit-learn', 'tqdm']]) + +exts_list = [ + ('pooch', '1.6.0', { + 'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'], + }), + ('coverage', '5.5', { + 'checksums': ['ebe78fe9a0e874362175b02371bdfbee64d8edc42a044253ddf4ee7d3c15212c'], + }), + ('pyriemann', '0.2.7', { + 'checksums': ['1feed8f72d94414bdc9ca4485333711a3f91f9742ae8794874a7399f4166758a'], + }), + ('moabb', version, { + 'preinstallopts': "sed -i '%s' pyproject.toml &&" % _relax_req, + 'checksums': ['4278be10aa721ba3ced0b03037901cccfeaeca6d04f7a157f1cf42f60395757d'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb index c4ae75df7095..134fe42c2052 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb @@ -32,7 +32,8 @@ exts_list = [ 'preinstallopts': 'BUILD_MONAI=1', 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], - 'checksums': ['dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b'], + 'checksums': [('dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b', + 'bb1a84ea3c4cd2c3756f72359a891843e0efa02da17537fb158b28c4e0b2d243')], }), ] diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb index 0314fc871d40..04560e4c6fdd 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb @@ -30,7 +30,8 @@ exts_list = [ 'preinstallopts': 'BUILD_MONAI=1', 'source_tmpl': '%(version)s.tar.gz', 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], - 'checksums': ['dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b'], + 'checksums': [('dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b', + 'bb1a84ea3c4cd2c3756f72359a891843e0efa02da17537fb158b28c4e0b2d243')], }), ] diff --git a/easybuild/easyconfigs/m/MPB/MPB-1.11.1-foss-2020b.eb b/easybuild/easyconfigs/m/MPB/MPB-1.11.1-foss-2020b.eb new file mode 100644 index 000000000000..bff6686a3209 --- /dev/null +++ b/easybuild/easyconfigs/m/MPB/MPB-1.11.1-foss-2020b.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'MPB' +version = '1.11.1' + +homepage = 'https://mpb.readthedocs.io/en/latest/' +description = """MPB is a free and open-source software package for computing + the band structures, or dispersion relations, and electromagnetic + modes of periodic dielectric structures, on both serial + and parallel computers. MPB is an acronym for MIT Photonic Bands.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://github.com/NanoComp/mpb/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dc55b081c56079727dac92d309f8e4ea84ca6eea9122ec24b7955f8c258608e1'] + +builddependencies = [ + ('Autotools', '20200321'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('HDF5', '1.10.7'), + ('libctl', '4.5.1'), + ('Guile', '3.0.9'), + ('libreadline', '8.0'), +] + +local_common_configopts = "--with-pic --with-blas=openblas --with-lapack=openblas " +local_common_configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared " + +configopts = [ + local_common_configopts + " ", + local_common_configopts + " --with-inv-symmetry", + local_common_configopts + " --with-mpi ", + local_common_configopts + " --with-mpi --with-inv-symmetry", +] + +sanity_check_paths = { + 'files': ['bin/mpb%s' % x for x in ['', '-data', 'i', 'i-data', 'i-mpi', 'i-split', '-mpi', '-split']] + + ['lib/libmpb.a', 'lib/libmpbi_mpi.a', 'lib/libmpbi.a', 'lib/libmpb_mpi.a', 'lib/libmpb.%s' % SHLIB_EXT, + 'lib/libmpbi_mpi.%s' % SHLIB_EXT, 'lib/libmpbi.%s' % SHLIB_EXT, 'lib/libmpb_mpi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/m/MRPRESSO/MRPRESSO-1.0-20230502-foss-2022a.eb b/easybuild/easyconfigs/m/MRPRESSO/MRPRESSO-1.0-20230502-foss-2022a.eb new file mode 100644 index 000000000000..710f1feccad8 --- /dev/null +++ b/easybuild/easyconfigs/m/MRPRESSO/MRPRESSO-1.0-20230502-foss-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'MRPRESSO' +# In spite of the repo name, everything else refers to MRPRESSO +local_commit = 'cece763' +# see DESCRIPTION to determine version, +# but also take date of last commit into account (since version isn't always bumped) +version = '1.0-20230502' + +homepage = 'https://github.com/rondolab/MR-PRESSO' +description = "Performs the Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO) method.." + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/rondolab/MR-PRESSO/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['f6c464f239eaf6341ac19bde272b3b1c0700013c32bcf480c1a2f18d177b630f'] + +dependencies = [ + ('R', '4.2.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-intel-2021a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-intel-2021a-metis.eb new file mode 100644 index 000000000000..fa811d068f92 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-intel-2021a-metis.eb @@ -0,0 +1,38 @@ +## +# Author: Robert Mijakovic +## +name = 'MUMPS' +version = '5.4.0' +versionsuffix = '-metis' + +homepage = 'https://graal.ens-lyon.fr/MUMPS/' +description = "A parallel sparse direct solver" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] +sources = ['%(name)s_%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD + '%(name)s-%(version)s_shared-mumps.patch', # builds shared libs of MUMPS +] +checksums = [ + 'c613414683e462da7c152c131cebf34f937e79b30571424060dd673368bbf627', # MUMPS_5.4.0.tar.gz + '4c0558690998c12ca959c03856054a75e22f519583a65bd550393c1f81a0b170', # MUMPS-5.4.0_shared-pord.patch + 'd51c2df0de7d7b88d864ceba2d0eea46c755c24c7124003481aced106901109d', # MUMPS-5.4.0_shared-mumps.patch +] + +dependencies = [ + ('SCOTCH', '6.1.0'), + ('METIS', '5.1.0'), +] + +parallel = 1 + +# fix 'Type mismatch between actual argument' errors with GCC 10.x +prebuildopts = 'export FFLAGS="$FFLAGS -fallow-argument-mismatch" && ' + +buildopts = 'all SONAME_VERSION="%(version)s"' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..f11b43042ac3 --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '5.1.0' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'rcedgar' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['2bba8b06e3ccabf6465fa26f459763b2029d7e7b9596881063e3aaba60d9e87d'] + +builddependencies = [ + ('binutils', '2.38'), +] + +start_dir = 'src' + +# Use build environment defined by EasyBuild +prebuildopts = "sed -i 's/$(CPPOPTS)/$(CPPOPTS) $(CXXFLAGS) $(CPPFLAGS)/g' Makefile &&" +buildopts = "CPP=${CXX} CC=${CC}" + +files_to_copy = [(['Linux/muscle'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/muscle'], + 'dirs': [], +} + +sanity_check_commands = ["muscle -h"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb new file mode 100644 index 000000000000..37fce889bdce --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.11.2-GCC-12.2.0.eb @@ -0,0 +1,68 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.11.2' + +homepage = 'https://mariadb.org/' +description = """MariaDB is an enhanced, drop-in replacement for MySQL. +Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = [ + 'https://archive.mariadb.org/mariadb-%(version)s/source/', + 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', +] +sources = [SOURCELOWER_TAR_GZ] +patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] +checksums = [ + {'mariadb-10.11.2.tar.gz': '1c89dee0caed0f68bc2a1d203eb98a123150e6a179f6ee0f1fc0ba3f08dc71dc'}, + {'MariaDB-10.1.13-link-rt-for-jemalloc.patch': '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('libaio', '0.3.113'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('LZO', '2.10'), # optional + ('lz4', '1.9.4'), # optional + ('XZ', '5.2.7'), # optional + ('jemalloc', '5.3.0'), # optional + ('snappy', '1.1.9'), # needed by RocksDB; optional for InnoDB + ('libxml2', '2.10.3'), # needed by Connect XML + ('Boost', '1.81.0'), # needed by OQGraph + ('Judy', '1.0.5'), # needed by OQGraph + ('PCRE2', '10.40'), + ('OpenSSL', '1.1', '', SYSTEM), # runtime dep for mysql and PCRE2 for mysqltest +] + +separate_build_dir = True + +configopts = "-DCMAKE_BUILD_TYPE=Release " +configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker +configopts += "-DMYSQL_MAINTAINER_MODE=OFF " # disabled to not treat warnings as errors (-Werror) +configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we build PCRE2 directly. +configopts += "-DWITH_ZLIB=system " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co +configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc + +sanity_check_commands = ["mysql --help", "mysqltest --help"] + +sanity_check_paths = { + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'lib/plugin/ha_connect.%s' % SHLIB_EXT, 'lib/plugin/ha_rocksdb.%s' % SHLIB_EXT, + 'lib/plugin/ha_oqgraph.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'dirs': ['include', 'share'], +} + +modextrapaths = {'PATH': 'scripts'} + +# Ensure that jemalloc does not use transparent hugepages. +# Database workloads with THP can cause memory bloat, potentially hiting OOM errors. +modextravars = {'MALLOC_CONF': 'thp:never'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb b/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb new file mode 100644 index 000000000000..0b54a7600994 --- /dev/null +++ b/easybuild/easyconfigs/m/Meep/Meep-1.26.0-foss-2020b.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'Meep' +version = '1.26.0' + +homepage = 'https://meep.readthedocs.io/en/latest/' +description = """Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package + developed at MIT to model electromagnetic systems.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['https://github.com/NanoComp/meep/releases/download/v%(version)s/'] +sources = ['meep-%(version)s.tar.gz'] +checksums = ['3f89f1bd781e46b938aa02e315a4526a4ae9896687db75c187b4f17febcbc301'] + +builddependencies = [ + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), + ('SWIG', '4.0.2') +] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('MPB', '1.11.1'), + ('Harminv', '1.4.2'), + ('HDF5', '1.10.7'), + ('libctl', '4.5.1'), + ('libGDSII', '0.21'), + ('GSL', '2.6'), + ('Guile', '3.0.9'), +] + +configopts = "--with-pic --with-mpi --with-blas=openblas --with-lapack=openblas --without-gcc-arch " +configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared " + +sanity_check_paths = { + 'files': ['bin/meep', 'include/meep.hpp', 'lib/libmeep.a', 'lib/libpympb.a', + 'lib/libmeep.%s' % SHLIB_EXT, 'lib/libpympb.%s' % SHLIB_EXT], + 'dirs': ['include/meep', 'lib/python%(pyshortver)s/site-packages/meep', 'share/meep'], +} + +sanity_check_commands = [ + "meep --help", + "python -c 'import meep'", +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb new file mode 100644 index 000000000000..16e6771ac7d7 --- /dev/null +++ b/easybuild/easyconfigs/m/MetaPhlAn/MetaPhlAn-4.0.6-foss-2022a.eb @@ -0,0 +1,48 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO + +easyblock = 'PythonBundle' + +name = 'MetaPhlAn' +version = '4.0.6' + +homepage = 'https://github.com/biobakery/MetaPhlAn' +description = """MetaPhlAn is a computational tool for profiling the composition + of microbial communities from metagenomic shotgun sequencing data """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Biopython', '1.79'), + ('Pysam', '0.19.1'), + ('DendroPy', '4.5.2'), + ('CMSeq', '1.0.4'), + ('biom-format', '2.1.14'), + ('h5py', '3.7.0'), + ('PhyloPhlAn', '3.0.3'), +] + +use_pip = True + +exts_list = [ + ('hclust2', '1.0.0', { + 'checksums': ['9667f1d16628940aedd3d1d571b956a6f77795018e3ea4dd83f234419eb0096d'], + }), + (name, version, { + 'checksums': ['e810d6b894ec6d0029255407f03a7dea1753ff65bde333ab34b40544cfb5553e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'strainphlan']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = ["metaphlan -h"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb new file mode 100644 index 000000000000..dbe91a2e7ff9 --- /dev/null +++ b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021b.eb @@ -0,0 +1,42 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +# Updated to foss 2021b: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'MoviePy' +version = '1.0.3' + +homepage = "https://zulko.github.io/moviepy/" +description = """MoviePy (full documentation) is a Python library for video editing: cutting, concatenations, + title insertions, video compositing (a.k.a. non-linear editing), video processing, and creation of custom effects.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('FFmpeg', '4.3.2'), + ('Python', '3.9.6'), + ('Pillow', '8.3.2'), + ('SciPy-bundle', '2021.10'), + ('tqdm', '4.62.3'), + ('imageio', '2.13.5'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('imageio-ffmpeg', '0.4.7', { + 'checksums': ['7a08838f97f363e37ca41821b864fd3fdc99ab1fe2421040c78eb5f56a9e723e'], + }), + ('proglog', '0.1.10', { + 'checksums': ['658c28c9c82e4caeb2f25f488fff9ceace22f8d69b15d0c1c86d64275e4ddab4'], + }), + (name, version, { + 'source_tmpl': 'moviepy-%(version)s.tar.gz', + 'patches': ['moviepy-1.0.3-setup.py.patch'], + 'checksums': [('2884e35d1788077db3ff89e763c5ba7bfddbd7ae9108c9bc809e7ba58fa433f5'), + ('beca82ff8dfbc9cd0b97296f310de3ddfc43e2e49344a32375d4438485c3f3df')], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.5.2.eb new file mode 100644 index 000000000000..3f167192cb4a --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.6.2-foss-2021b-CUDA-11.5.2.eb @@ -0,0 +1,42 @@ +easyblock = "CMakeMake" + +name = 'magma' +version = '2.6.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://icl.cs.utk.edu/magma/' +description = """The MAGMA project aims to develop a dense linear algebra library similar to + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://icl.cs.utk.edu/projectsfiles/magma/downloads/'] +sources = [SOURCE_TAR_GZ] +patches = ['magma-2.6.1_allow-all-sms.patch'] +checksums = [ + '75b554dab00903e2d10b972c913e50e7f88cbc62f3ae432b5a086c7e4eda0a71', # magma-2.6.2.tar.gz + 'b89285bac007b68e88e3b5ddbb7f94dbc8a9d77590e58c352e477574d8dca738', # magma-2.6.1_allow-all-sms.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('CUDA', '11.5.2', '', SYSTEM), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6'] +# make sure both static and shared libs are built +configopts = [ + '-DBUILD_SHARED_LIBS=%s -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF') +] + +sanity_check_paths = { + 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/make/make-4.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/make/make-4.3-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..2d7194c63541 --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.3-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'make' +version = '4.3' + +homepage = 'https://www.gnu.org/software/make/make.html' +description = "GNU version of make utility" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e05fdde47c5f7ca45cb697e973894ff4f5d79e13b750ed57d7b66d8defc78e19'] + +builddependencies = [('binutils', '2.39')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] + +sanity_check_paths = { + 'files': ['bin/gmake', 'bin/make'], + 'dirs': [] +} + +sanity_check_commands = [ + "gmake --help", + "make --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..a4107e59ee5d --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'make' +version = '4.4.1' + +homepage = 'https://www.gnu.org/software/make/make.html' +description = "GNU version of make utility" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['dd16fb1d67bfab79a72f5e8390735c49e3e8e70b4945a15ab1f81ddb78658fb3'] + +builddependencies = [('binutils', '2.39')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] + +sanity_check_paths = { + 'files': ['bin/gmake', 'bin/make'], + 'dirs': [] +} + +sanity_check_commands = [ + "gmake --help", + "make --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..283fa0f57f8a --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.4.1-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'make' +version = '4.4.1' + +homepage = 'https://www.gnu.org/software/make/make.html' +description = "GNU version of make utility" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['dd16fb1d67bfab79a72f5e8390735c49e3e8e70b4945a15ab1f81ddb78658fb3'] + +builddependencies = [('binutils', '2.40')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] + +sanity_check_paths = { + 'files': ['bin/gmake', 'bin/make'], + 'dirs': [] +} + +sanity_check_commands = [ + "gmake --help", + "make --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb b/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb new file mode 100644 index 000000000000..d6860c0a27e0 --- /dev/null +++ b/easybuild/easyconfigs/m/mandrake/mandrake-1.2.2-foss-2022a.eb @@ -0,0 +1,52 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'mandrake' +version = '1.2.2' + +homepage = 'https://mandrake.readthedocs.io' +description = """Fast visualisation of the population structure of pathogens +using Stochastic Cluster Embedding.""" + +citing = """Lees JA, Tonkin-Hill G, Yang Z, Corander J. Mandrake: visualizing +microbial population structure by embedding millions of genomes into a +low-dimensional representation. +Philosophical Transactions of The Royal Society B. 2022;377: 20210237. +https://doi.org/10.1098/rstb.2021.0237""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('plotly.py', '5.12.0'), + ('matplotlib', '3.5.2'), + ('HDBSCAN', '0.8.29'), + ('h5py', '3.7.0'), + ('pp-sketchlib', '2.1.1'), + ('pybind11', '2.9.2'), + ('Eigen', '3.4.0'), + ('Boost', '1.79.0'), + ('tqdm', '4.64.0'), + ('FFmpeg', '4.4.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/bacpop/mandrake/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5bbdde903252e2812d4ba484ae474ccc75efbaaf0ace7fe6f37a90e44fe3f0e5'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2022a.eb b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2022a.eb new file mode 100644 index 000000000000..500f6c287a42 --- /dev/null +++ b/easybuild/easyconfigs/m/mapDamage/mapDamage-2.2.1-foss-2022a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'mapDamage' +version = '2.2.1' + +github_account = 'ginolhac' + +homepage = 'https://ginolhac.github.io/mapDamage/' +description = """mapDamage2 is a computational framework written in Python and + R, which tracks and quantifies DNA damage patterns among ancient DNA + sequencing reads generated by Next-Generation Sequencing platforms.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-2.2.1_use-external-seqtk.patch'] +checksums = [ + 'f86cd2b1fac3e6a1d6ccc97d37ef6cf3b5be07747c3d3894472a8d1da9eb595c', # 2.2.1.tar.gz + 'f01a90c29123460f8cb6ba2fe0f42e9ec66b0febff430d4ec4f0ab1197c552e7', # mapDamage-2.2.1_use-external-seqtk.patch +] + +dependencies = [ + ('Python', '3.10.4'), + ('seqtk', '1.3'), + ('Pysam', '0.19.1'), + ('R', '4.2.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_commands = ['mapDamage --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..026ff55fa14c --- /dev/null +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'mctc-lib' +version = '0.3.1' + +homepage = 'https://grimme-lab.github.io/mctc-lib' +description = """Common tool chain for working with molecular structure data in various +applications. This library provides a unified way to perform operations on +molecular structure data, like reading and writing to common geometry file +formats.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['03dc8ccba37413da70e55a07cef8e8de53bce33f5bb52c1f8db5fec326abe083'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=1' + +sanity_check_paths = { + 'files': ['bin/mctc-convert', 'lib/libmctc-lib.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mctc-convert --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/mold/mold-1.11.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/mold/mold-1.11.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..256cc29ec4c3 --- /dev/null +++ b/easybuild/easyconfigs/m/mold/mold-1.11.0-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'mold' +version = '1.11.0' + +homepage = 'https://github.com/rui314/mold' +description = "mold is a high-performance drop-in replacement for existing Unix linkers." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/rui314/mold/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['99318eced81b09a77e4c657011076cc8ec3d4b6867bd324b8677974545bc4d6f'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] +dependencies = [ + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/mold', 'lib/mold/mold-wrapper.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = [ + "mold --help", + "mold --run gcc -v", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2022a.eb b/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2022a.eb new file mode 100644 index 000000000000..b5ea22facf26 --- /dev/null +++ b/easybuild/easyconfigs/m/msprime/msprime-1.2.0-foss-2022a.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'msprime' +version = '1.2.0' + +homepage = 'https://msprime.readthedocs.io' +description = "msprime is a coalescent simulator and library for processing tree-based genetic data." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # for numpy + ('GSL', '2.7'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('svgwrite', '1.4.3', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['a8fbdfd4443302a6619a7f76bc937fc683daf2628d9b737c891ec08b8ce524c3'], + }), + ('tskit', '0.5.4', { + 'checksums': ['be1a6381c72a95f0011bea26ca317e1b4503b8d2dcd87096c68aa16c8946c6fe'], + }), + ('ruamel.yaml.clib', '0.2.7', { + 'modulename': False, + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + }), + ('ruamel.yaml', '0.17.21', { + 'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'], + }), + ('demes', '0.2.2', { + 'checksums': ['8eebe4b236b2d19e057228892f5b5f53f3e0d127ca9128efead1728a65115dac'], + }), + ('newick', '1.9.0', { + 'checksums': ['9f81be96ec86aefca74d920fc0d6962d89a3156547003ca6915c2e6e31ad3ddf'], + }), + (name, version, { + 'checksums': ['60025ad9fd30d827a72ae6e760b6cff07a1d0e169b2c1da1024cb0fc23e4a7aa'], + }), +] + +sanity_check_paths = { + 'files': ['bin/msp', 'bin/mspms', 'bin/tskit', 'bin/demes'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'demes --help', + 'tskit --help', + 'msp --help', + 'mspms --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..a8015f4cc5f4 --- /dev/null +++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'mstore' +version = '0.2.0' + +homepage = 'https://github.com/grimme-lab/mstore' +description = """Molecular structure store for testing""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['95edba88afbc8013f57f4c818a97c0500cc40b158bed11234c061b2b6d7e480d'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=1' + +sanity_check_paths = { + 'files': ['bin/mstore-fortranize', 'bin/mstore-info', 'lib/libmstore.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mstore-info --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..f20ab6b457e0 --- /dev/null +++ b/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'muParser' +version = '2.3.4' + +homepage = 'https://beltoforion.de/article.php?a=muparser' +description = """ + muParser is an extensible high performance math expression parser library + written in C++. It works by transforming a mathematical expression into + bytecode and precalculating constant parts of the expression. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/beltoforion/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0c3fa54a3ebf36dda0ed3e7cd5451c964afbb15102bdbcba08aafb359a290121'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +configopts = "-DENABLE_SAMPLES=OFF -DBUILD_SHARED_LIBS=ON" + + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/libmuparser.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NAG/NAG-7.1-gompi-2022b.eb b/easybuild/easyconfigs/n/NAG/NAG-7.1-gompi-2022b.eb new file mode 100644 index 000000000000..dd7e50c3ced6 --- /dev/null +++ b/easybuild/easyconfigs/n/NAG/NAG-7.1-gompi-2022b.eb @@ -0,0 +1,30 @@ +easyblock = 'Binary' + +name = 'NAG' +version = '7.1' + +homepage = 'http://www.nag.co.uk' +description = "The worlds largest collection of robust, documented, tested and maintained numerical algorithms." + +toolchain = {'name': 'gompi', 'version': '2022b'} + +sources = [{ + 'source_urls': ['https://www.nag.co.uk/downloads/impl'], + 'filename': SOURCE_TGZ, + 'download_filename': 'npl6a%(version_major)s%(version_minor)sna_amd64.tgz' +}] +checksums = ['0f173ea0e0809673db216622a7354cc2eb52bf13372a34ef85e62a115bb6f94f'] + +extract_sources = True + +install_cmd = "INSTALL_TO_BINDIR=%(installdir)s/bin INSTALL_TO_LIBDIR=%(installdir)s/lib " +install_cmd += "INSTALL_TO_CATMANDIR=%(installdir)s/man INSTALL_TO_MANDIR=%(installdir)s/man ./INSTALLU.sh" + +modextravars = {'NAG_KUSARI_FILE': HOME + '/licenses/license.dat'} + +sanity_check_paths = { + 'files': ['bin/dbx90', 'bin/nagfmcheck', 'bin/nagfor'], + 'dirs': ['lib', 'man1', 'man3'], +} + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/n/NAGfor/NAGfor-7.1.eb b/easybuild/easyconfigs/n/NAGfor/NAGfor-7.1.eb new file mode 100644 index 000000000000..3560fb4a9950 --- /dev/null +++ b/easybuild/easyconfigs/n/NAGfor/NAGfor-7.1.eb @@ -0,0 +1,30 @@ +easyblock = 'Binary' + +name = 'NAGfor' +version = '7.1' + +homepage = 'http://www.nag.co.uk' +description = """The checking compiler for improved code portability and detailed error reporting.""" + +toolchain = SYSTEM + +sources = [{ + 'source_urls': ['https://www.nag.co.uk/downloads/impl'], + 'filename': SOURCE_TGZ, + 'download_filename': 'npl6a%(version_major)s%(version_minor)sna_amd64.tgz' +}] +checksums = ['0f173ea0e0809673db216622a7354cc2eb52bf13372a34ef85e62a115bb6f94f'] + +extract_sources = True + +install_cmd = "INSTALL_TO_BINDIR=%(installdir)s/bin INSTALL_TO_LIBDIR=%(installdir)s/lib " +install_cmd += "INSTALL_TO_CATMANDIR=%(installdir)s/man INSTALL_TO_MANDIR=%(installdir)s/man ./INSTALLU.sh" + +modextravars = {'NAG_KUSARI_FILE': HOME + '/licenses/license.dat'} + +sanity_check_paths = { + 'files': ['bin/dbx90', 'bin/nagfmcheck', 'bin/nagfor'], + 'dirs': ['lib', 'man1', 'man3'], +} + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.16.01-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.16.01-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..5c1bbfafd36f --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.16.01-GCCcore-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.16.01' + +homepage = 'https://www.nasm.us/' + +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['35b6ad2ee048d41c4779f073f3efca7762a822b7d2d4ef4e8df24cf65747bb2e'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb new file mode 100644 index 000000000000..e3a29b13334a --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.10.3-GCCcore-11.2.0-CUDA-11.5.2.eb @@ -0,0 +1,23 @@ +name = 'NCCL' +version = '2.10.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +checksums = ['55de166eb7dcab9ecef2629cdb5fb0c5ebec4fae03589c469ebe5dcb5716b3c5'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('CUDA', '11.5.2', '', SYSTEM), + ('UCX-CUDA', '1.11.2', versionsuffix), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..a5ee868d2414 --- /dev/null +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'NSPR' +version = '4.35' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR' +description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level + and libc-like functions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.mozilla.org/pub/nspr/releases/v%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7ea3297ea5969b5d25a5dd8d47f2443cda88e9ee746301f6e1e1426f8a6abc8f'] + +builddependencies = [('binutils', '2.40')] + +configopts = "--disable-debug --enable-optimize --enable-64bit" + +sanity_check_paths = { + 'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/nspr.pc'], + 'dirs': ['include/nspr'], +} + +sanity_check_commands = ["nspr-config --version"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..7b9beb5c0864 --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb @@ -0,0 +1,61 @@ +easyblock = 'MakeCp' + +name = 'NSS' +version = '3.89.1' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' +description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development + of security-enabled client and server applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%s_RTM/src/' % version.replace('.', '_')] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'NSS-3.39_pkgconfig.patch', + 'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch', +] +checksums = [ + {'nss-3.89.1.tar.gz': '3adaedb9e70c3c5f40603bf60a01e336190a6dbe01929d395f16b01fe84a0156'}, + {'NSS-3.39_pkgconfig.patch': '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774'}, + {'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch': + '15768297c5dd6918132af281531afcfe3e358f45a00bc2655d20a6cbe4310a9b'}, +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('NSPR', '4.35'), + ('zlib', '1.2.13'), +] + +# building in parallel fails +parallel = 1 + +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = "NSS_ENABLE_WERROR=0 " +# fix for not being able to find header files +buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +# fix c standard causing missing functions +buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' +# also install pkgconfig file (see patch) +buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" +# optional testsuite (takes a long time) +# buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && BUILD_OPT=1 USE_64=1 ./all.sh " + +files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] + +sanity_check_paths = { + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], +} + +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + +modextrapaths = {'CPATH': 'include/nss'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.2.0.eb b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.2.0.eb new file mode 100644 index 000000000000..cbeb836cd913 --- /dev/null +++ b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.2.0.eb @@ -0,0 +1,44 @@ +# contributed by Guilherme Peretti-Pezzi (CSCS) +# updated by Alex Domingo (Vrije Universiteit Brussel) +# updated by Åke Sandgren(Umeå University) + +easyblock = 'ConfigureMake' + +name = 'NTL' +version = '11.5.1' + +homepage = 'https://shoup.net/ntl/' + +description = """NTL is a high-performance, portable C++ library providing data structures and +algorithms for manipulating signed, arbitrary length integers, and for vectors, +matrices, and polynomials over the integers and over finite fields.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'libntl' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ef578fa8b6c0c64edd1183c4c303b534468b58dd3eb8df8c9a5633f984888de5'] + +builddependencies = [ + ('Perl', '5.34.0'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +start_dir = 'src' + +prefix_opt = 'PREFIX=' +configopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS" GMP_PREFIX="$EBROOTGMP" SHARED=on' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libntl.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['include/NTL', 'share/doc'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.3.0.eb b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.3.0.eb new file mode 100644 index 000000000000..89c7288994f1 --- /dev/null +++ b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-11.3.0.eb @@ -0,0 +1,44 @@ +# contributed by Guilherme Peretti-Pezzi (CSCS) +# updated by Alex Domingo (Vrije Universiteit Brussel) +# updated by Åke Sandgren(Umeå University) + +easyblock = 'ConfigureMake' + +name = 'NTL' +version = '11.5.1' + +homepage = 'https://shoup.net/ntl/' + +description = """NTL is a high-performance, portable C++ library providing data structures and +algorithms for manipulating signed, arbitrary length integers, and for vectors, +matrices, and polynomials over the integers and over finite fields.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'libntl' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ef578fa8b6c0c64edd1183c4c303b534468b58dd3eb8df8c9a5633f984888de5'] + +builddependencies = [ + ('Perl', '5.34.1'), +] + +dependencies = [ + ('GMP', '6.2.1'), +] + +start_dir = 'src' + +prefix_opt = 'PREFIX=' +configopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS" GMP_PREFIX="$EBROOTGMP" SHARED=on' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libntl.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['include/NTL', 'share/doc'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/nano/nano-7.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nano/nano-7.2-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..99cb4947e273 --- /dev/null +++ b/easybuild/easyconfigs/n/nano/nano-7.2-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'nano' +version = '7.2' + +homepage = 'https://www.nano-editor.org/' +docurls = 'https://www.nano-editor.org/docs.php' +description = """a simple editor, inspired by Pico""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.nano-editor.org/dist/v%(version_major)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b4edaab0a037b5760484907c674e980053896f33759e43f834a212145fd085f1'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('ncurses', '6.3')] + +sanity_check_paths = { + 'files': ['bin/nano'], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = ['nano --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..b1731393710a --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-12.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.4' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6931283d9ac87c5073f30b6290c4c75f21632bb4fc3603ac8100812bed248159'] + +builddependencies = [('binutils', '2.40')] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " +configopts = [ + # build ncurses: serial build in default paths with shared libraries + local_common_configopts, + # build ncursesw: serial with UTF-8 + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-13.1.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..edca9ab59549 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.4-GCCcore-13.1.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.4' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """ + The Ncurses (new curses) library is a free software emulation of curses in + System V Release 4.0, and more. It uses Terminfo format, supports pads and + color and multiple highlights and forms characters and function-key mapping, + and has all the other SYSV-curses enhancements over BSD Curses. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6931283d9ac87c5073f30b6290c4c75f21632bb4fc3603ac8100812bed248159'] + +builddependencies = [('binutils', '2.40')] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks --with-versioned-syms " +configopts = [ + # build ncurses: serial build in default paths with shared libraries + local_common_configopts, + # build ncursesw: serial with UTF-8 + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# Symlink libtinfo to libncurses +# libncurses with this configopts has all the symbols from libtinfo, but some packages look for libtinfo specifically +postinstallcmds = ['cd %(installdir)s/lib && for l in libncurses{.,_,w}*; do ln -s "${l}" "${l/ncurses/tinfo}"; done'] + +_target_suffix = ['', 'w'] # '': ncurses, 'w': ncursesw +_lib_suffix = ['%s%s' % (x, y) for x in _target_suffix for y in ['.a', '_g.a', '.' + SHLIB_EXT]] +_lib_names = ['form', 'menu', 'ncurses', 'panel', 'tinfo'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s' % (x, y) for x in _lib_names for y in _lib_suffix] + + ['lib/libncurses++%s.a' % x for x in _target_suffix], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022b.eb new file mode 100644 index 000000000000..e7d505dc509f --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-gompi-2022b.eb @@ -0,0 +1,28 @@ +name = 'netCDF-Fortran' +version = '4.6.0' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8194aa70e400c0adfc456127c1d97af2c6489207171d13b10cd754a16da8b0ca'] + +builddependencies = [ + ('M4', '1.4.19'), +] + +dependencies = [ + ('netCDF', '4.9.0'), + ('bzip2', '1.0.8'), +] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.3-foss-2022b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.3-foss-2022b.eb new file mode 100644 index 000000000000..ef656081b80e --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.3-foss-2022b.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.6.3' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('netCDF', '4.9.0'), + ('cURL', '7.86.0'), + ('mpi4py', '3.1.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.6.2', { + 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], + }), + (name, version, { + 'patches': [ + 'netcdf4-python-1.1.8-avoid-diskless-test.patch', + 'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch', + ], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + {'netCDF4-1.6.3.tar.gz': '8c98a3a8cda06920ee8bd24a71226ddf0328c22bd838b0afca9cb45fb4580d99'}, + {'netcdf4-python-1.1.8-avoid-diskless-test.patch': + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72'}, + {'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch': + '64d192a5d1e3e00af78f053da78f5a35015fa713c7f97b10b622be6a44347166'}, + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.8.8-gfbf-2022b.eb b/easybuild/easyconfigs/n/networkx/networkx-2.8.8-gfbf-2022b.eb new file mode 100644 index 000000000000..bac13dc9e35a --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.8.8-gfbf-2022b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.8.8' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['230d388117af870fce5647a3c52401fcf753e94720e6ea6b4197a5355648885e'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..1ad7b6c1af63 --- /dev/null +++ b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.2-GCCcore-12.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'nlohmann_json' +version = '3.11.2' + +homepage = 'https://github.com/nlohmann/json' +description = """JSON for Modern C++""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/nlohmann/json/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d69f9deb6a75e2580465c6c4c5111b89c4dc2fa94e3a85fcd2ffcd9a143d9273'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['include/nlohmann/json.hpp'], + 'dirs': ['share/cmake', 'share/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..68237d4c0cc2 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.16-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.16' + +homepage = 'https://github.com/numactl/numactl' + +description = """ + The numactl program allows you to run your application program on specific + cpu's and memory nodes. It does this by supplying a NUMA memory policy to + the operating system before running your program. The libnuma library provides + convenient ways for you to add NUMA memory policies into your own program. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/numactl/numactl/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['1b242f893af977a1d31af6ce9d6b8dafdd2d8ec3dc9207f7c2dc0d3446e7c7c8'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.8.4-foss-2022a.eb b/easybuild/easyconfigs/n/numexpr/numexpr-2.8.4-foss-2022a.eb new file mode 100644 index 000000000000..41f638503e2c --- /dev/null +++ b/easybuild/easyconfigs/n/numexpr/numexpr-2.8.4-foss-2022a.eb @@ -0,0 +1,21 @@ +name = 'numexpr' +version = '2.8.4' + +homepage = 'https://numexpr.readthedocs.io/en/latest/' +description = """The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. + It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into + code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a + compiler at runtime.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/pydata/numexpr/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0e21addd25db5f62d60d97e4380339d9c1fb2de72c88b070c279776ee6455d10'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..c4dd3f56af6e --- /dev/null +++ b/easybuild/easyconfigs/n/nvtop/nvtop-3.0.1-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'nvtop' +version = '3.0.1' + +homepage = 'https://github.com/Syllo/nvtop' +description = 'htop-like GPU usage monitor' + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/Syllo/nvtop/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f61ecbe3a30a216706c16fc177d3b840e7d7deccf87b048d59f95f230d591a53'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +# Note: software dlopen's libraries from the OS installed drivers, thus no specific CUDA dependency. +dependencies = [ + ('ncurses', '6.3'), + ('libdrm', '2.4.114'), +] + +osdependencies = [('libsystemd-dev', 'libudev-dev', 'systemd-devel')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/nvtop'], + 'dirs': [], +} + +sanity_check_commands = ["nvtop --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb index c98d769985ef..48333ab642d1 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.12-GCC-10.2.0.eb @@ -31,6 +31,10 @@ checksums = [ '9cc47898ba4ad090011dbb0b29e597a13eeebd49a52d4dc94e975743072724b7', ] +builddependencies = [ + ('make', '4.3'), +] + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb index 3b8d83f4116d..13b731bc6d1f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.15-GCC-10.3.0.eb @@ -29,6 +29,10 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] +builddependencies = [ + ('make', '4.3'), +] + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb index ae8fd51485ed..a7984cac146a 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-10.3.0.eb @@ -25,6 +25,10 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', ] +builddependencies = [ + ('make', '4.3'), +] + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index c4b29c67422f..1df506125c23 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -39,6 +39,7 @@ checksums = [ ] builddependencies = [ + ('make', '4.3'), # required by LAPACK test suite ('Python', '3.9.6', '-bare'), ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index 762a9558bfb9..e00c62b1089c 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -36,6 +36,7 @@ checksums = [ ] builddependencies = [ + ('make', '4.3'), # required by LAPACK test suite ('Python', '3.9.6', '-bare'), ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index 98f44c83e7ce..ad53aa70e6bb 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -34,6 +34,7 @@ checksums = [ ] builddependencies = [ + ('make', '4.3'), # required by LAPACK test suite ('Python', '3.9.6', '-bare'), ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index 4496c0bc5b3f..c00bedf7a63e 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -34,6 +34,7 @@ checksums = [ ] builddependencies = [ + ('make', '4.3'), # required by LAPACK test suite ('Python', '3.10.4', '-bare'), ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb index 39645058d21d..7b49821c3487 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb @@ -33,6 +33,10 @@ checksums = [ {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] +builddependencies = [ + ('make', '4.3'), +] + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb index b0244cb98cef..274aeeec351b 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb @@ -34,6 +34,7 @@ checksums = [ ] builddependencies = [ + ('make', '4.3'), # required by LAPACK test suite ('Python', '3.10.8', '-bare'), ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb index c390c260b685..0e4b7e6439e4 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb @@ -36,6 +36,10 @@ checksums = [ '9210a94ae418b4ce6d9f7fab4e00dd3155451f5ef3769536a4d954a2149ca733', # OpenBLAS-0.3.9_fix-lapack_h.patch ] +builddependencies = [ + ('make', '4.3'), +] + # extensive testing can be enabled by uncommenting the line below # runtest = 'PATH=.:$PATH lapack-timing' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb index 70276c875266..4ca1c26a38c2 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb @@ -32,10 +32,13 @@ sources = [ 'extract_cmd': 'cp %s %(builddir)s' }, ] +patches = [('opencv_contrib_python.egg-info', '..')] checksums = [ - '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip - '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip - '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz + {'opencv-4.6.0.zip': '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359'}, + {'opencv_contrib-4.6.0.zip': '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3'}, + {'ippicv_2020_lnx_intel64_20191018_general.tgz': + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246'}, + {'opencv_contrib_python.egg-info': '08eb95c735d4ff82e35e3df56c2e7e75501cc263a8efcb9348d04e6322a4b034'}, ] builddependencies = [ @@ -68,6 +71,7 @@ dependencies = [ # ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 configopts = " ".join([ "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", + "-DOPENCV_GENERATE_PKGCONFIG=ON", "-DFREETYPE_FOUND=ON", "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", @@ -82,6 +86,13 @@ configopts = " ".join([ "-DCUDA_NVCC_FLAGS=--std=c++14", ]) +# Install a egg-info file so it is more python friendly +local_egg_info_src = '%(builddir)s/opencv_contrib_python.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/opencv_contrib_python-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#OPENCV_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + enhance_sanity_check = True local_contrib_libs = [ diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb index b957c01b7d4c..f71431e0f088 100644 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -31,10 +31,13 @@ sources = [ 'extract_cmd': 'cp %s %(builddir)s' }, ] +patches = [('opencv_contrib_python.egg-info', '..')] checksums = [ - '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip - '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip - '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz + {'opencv-4.6.0.zip': '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359'}, + {'opencv_contrib-4.6.0.zip': '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3'}, + {'ippicv_2020_lnx_intel64_20191018_general.tgz': + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246'}, + {'opencv_contrib_python.egg-info': '08eb95c735d4ff82e35e3df56c2e7e75501cc263a8efcb9348d04e6322a4b034'}, ] builddependencies = [ @@ -65,6 +68,7 @@ dependencies = [ # ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 configopts = " ".join([ "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", + "-DOPENCV_GENERATE_PKGCONFIG=ON", "-DFREETYPE_FOUND=ON", "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", @@ -78,6 +82,13 @@ configopts = " ".join([ "-DBUILD_opencv_python2=OFF", ]) +# Install a egg-info file so it is more python friendly +local_egg_info_src = '%(builddir)s/opencv_contrib_python.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/opencv_contrib_python-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#OPENCV_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + enhance_sanity_check = True local_contrib_libs = [ @@ -88,7 +99,7 @@ local_contrib_libs = [ ] sanity_check_paths = { - 'files': ['lib64/libopencv_%s.%s' % (s, SHLIB_EXT) for s in local_contrib_libs], + 'files': ['lib64/libopencv_%s.%s' % (x, SHLIB_EXT) for x in local_contrib_libs], 'dirs': [], } diff --git a/easybuild/easyconfigs/o/OpenCV/opencv_contrib_python.egg-info b/easybuild/easyconfigs/o/OpenCV/opencv_contrib_python.egg-info new file mode 100644 index 000000000000..073e127f34d7 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/opencv_contrib_python.egg-info @@ -0,0 +1,5 @@ +Metadata-Version: 2.1 +Name: opencv-contrib-python +Version: #OPENCV_VERSION# +Summary: Wrapper package for OpenCV python bindings. +Platform: UNKNOWN diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.7-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..f66f45d25c3a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.7-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.1.7' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['78dbca39115a1c526e6728588753955ee75fa7f5bb1a6e238bed5b6d66f91fd7'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] +dependencies = [ + ('Imath', '3.1.7'), + ('zlib', '1.2.13') +] + +local_libs, local_bins = [ + ['Iex', 'IlmThread', 'OpenEXR', 'OpenEXRUtil'], + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] +] + +sanity_check_paths = { + 'files': ( + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] + ), + 'dirs': ['include/%(name)s', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb new file mode 100644 index 000000000000..f9ebf346635a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a-20230119.eb @@ -0,0 +1,42 @@ +name = 'OpenFOAM' + +version = '10' +_version_patch = '20230119' +versionsuffix = '-%s' % _version_patch + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = [{ + 'download_filename': '%s.tar.gz' % _version_patch, + 'filename': 'OpenFOAM-%(version)s%(versionsuffix)s.tar.gz', +}] +patches = ['OpenFOAM-%(version_major)s-ThirdParty.patch'] +checksums = [ + {'OpenFOAM-10-20230119.tar.gz': '86f8cb18d4f59812b129ce7d669e8ff498da442fbdb46705492fbba3cbda82ab'}, + {'OpenFOAM-10-ThirdParty.patch': '307df0206cdb24533f4974378843332064f4a2d85cf0638c20fc4c87b1524b43'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('ncurses', '6.3'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.1'), + ('CGAL', '4.14.3'), + ('ParaView', '5.10.1', '-mpi'), + ('gnuplot', '5.4.4'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..1c0e9a28999c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.5.0' + +homepage = 'https://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0333806d6adecc6f7a91243b2b839ff4d2053823634d4f6ed7a59bc87409122a'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.38'), + ('LibTIFF', '4.4.0'), +] + +sanity_check_paths = { + 'files': [ + 'bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT + ], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..e930df38233b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.5.0' + +homepage = 'https://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0333806d6adecc6f7a91243b2b839ff4d2053823634d4f6ed7a59bc87409122a'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.2.13'), + ('libpng', '1.6.39'), + ('LibTIFF', '4.5.0'), +] + +sanity_check_paths = { + 'files': [ + 'bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT + ], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021b-CUDA-11.4.1-DeepMind-patch.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021b-CUDA-11.4.1-DeepMind-patch.eb new file mode 100644 index 000000000000..335b9a7e2daf --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-7.5.1-foss-2021b-CUDA-11.4.1-DeepMind-patch.eb @@ -0,0 +1,66 @@ +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '7.5.1' +versionsuffix = '-CUDA-%(cudaver)s-DeepMind-patch' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + ('OpenMM-%(version)s_DeepMind.patch', 'wrappers/python'), + 'OpenMM-7.5.0_fix_path_to_nvcc.patch', + 'OpenMM-8.0.0_add_no_tree_vectorize.patch', +] +checksums = [ + {'7.5.1.tar.gz': 'c88d6946468a2bde2619acb834f57b859b5e114a93093cf562165612e10f4ff7'}, + {'OpenMM-7.5.1_DeepMind.patch': '1b109dfff3af5c6aa70690bca14618612953c68840a7e64f679db7ca33c1aff6'}, + {'OpenMM-7.5.0_fix_path_to_nvcc.patch': '050d5b81e70b34d06ef87eafc6d540b2cf716a61f53b1d2a3786504da3ec2e3c'}, + {'OpenMM-8.0.0_add_no_tree_vectorize.patch': '4bacf45443a2472e59798743f27d07481e065d784cbbea7be22aa6427af0d2bd'}, +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('CUDA', '11.4.1', '', SYSTEM), + ('SWIG', '4.0.2'), +] + +# Flags for CUDA-enabled build +configopts = "-DOPENMM_BUILD_CUDA_LIB=ON" + +# defining OPENMM_CUDA_COMPILER=nvcc on pretestops causes 1 test to fail: https://github.com/openmm/openmm/issues/3373 +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/simtk/openmm/openmm.py'], + 'dirs': [] +} + +sanity_check_commands = ["python -m simtk.testInstallation"] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..4215d0a143f5 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,70 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '8.0.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['OpenMM-8.0.0_add_no_tree_vectorize.patch'] +checksums = [ + 'dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e', # 8.0.0.tar.gz + '4bacf45443a2472e59798743f27d07481e065d784cbbea7be22aa6427af0d2bd', # OpenMM-8.0.0_add_no_tree_vectorize.patch +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('SWIG', '4.0.2'), + ('CUDA', '11.7.0', '', SYSTEM), +] + +# Set the OPENMM_CUDA_COMPILER variable to make sure that all tests use the right nvcc, +# Otherwise they will use the wrong path: `/usr/local/cuda/bin/nvcc` +pretestopts = ' export OPENMM_CUDA_COMPILER=${EBROOTCUDA}/bin/nvcc && ' +pretestopts += " CTEST_OUTPUT_ON_FAILURE=1" +# Skip CudaCompiler test as it doesn't work when the OPENMM_CUDA_COMPILER variable is set +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)|(CudaCompiler)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + "python -c 'import simtk.openmm'", + "python -m openmm.testInstallation", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb new file mode 100644 index 000000000000..47d3bdbfaf54 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0-foss-2022a.eb @@ -0,0 +1,60 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '8.0.0' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['dc63d7b47c8bb7b169c409cfd63d909ed0ce1ae114d37c627bf7a4231acf488e'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('SWIG', '4.0.2'), +] + +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + "python -c 'import simtk.openmm'", + "python -m openmm.testInstallation", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0_add_no_tree_vectorize.patch b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0_add_no_tree_vectorize.patch new file mode 100644 index 000000000000..e3fb0d995791 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.0.0_add_no_tree_vectorize.patch @@ -0,0 +1,16 @@ +# This patch resolves the tree vectorizatior error that appears when "-march" is used with GCC 11.3.0: +# .../openmm-8.0.0/platforms/common/src/CommonKernels.cpp:5055:6: internal compiler error: in vect_get_vec_defs_for_operand, at tree-vect-stmts.c:1450 +# 5055 | void CommonCalcGayBerneForceKernel::sortAtoms() { +# Author: maxim-masterov (SURF) + +diff -Nru openmm-8.0.0.orig/platforms/common/src/CommonKernels.cpp openmm-8.0.0/platforms/common/src/CommonKernels.cpp +--- openmm-8.0.0.orig/platforms/common/src/CommonKernels.cpp 2023-03-29 10:08:28.765461000 +0200 ++++ openmm-8.0.0/platforms/common/src/CommonKernels.cpp 2023-04-04 15:55:17.152316000 +0200 +@@ -5052,6 +5052,7 @@ + sortAtoms(); + } + ++__attribute__((optimize("no-tree-vectorize"))) + void CommonCalcGayBerneForceKernel::sortAtoms() { + // Sort the list of atoms by type to avoid thread divergence. This is executed every time + // the atoms are reordered. diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-iomkl-2021a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-iomkl-2021a.eb new file mode 100644 index 000000000000..2de233814bfc --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-21.06-iomkl-2021a.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'OpenMolcas' +version = '21.06' + +homepage = 'https://gitlab.com/Molcas/OpenMolcas' +description = "OpenMolcas is a quantum chemistry software package" + +toolchain = {'name': 'iomkl', 'version': '2021a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://gitlab.com/Molcas/%(name)s/-/archive/v%(version)s/'] +sources = ['%(name)s-v%(version)s.tar.gz'] +patches = ['%(name)s-21.06_mcpdft_deps.patch'] +checksums = [ + '54cf989c1e0fcb7e8927f0c64fe356b300bf3537e4868356eea47105a8a06e3a', # %(name)s-v21.06.tar.gz + '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a', # %(name)s-21.06_mcpdft_deps.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), +] +dependencies = [ + ('GlobalArrays', '5.8'), + ('HDF5', '1.10.7'), + ('Python', '3.9.5'), +] + +preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' +configopts = "-DLINALG=MKL -DMKLROOT=$MKLROOT -DMPI=ON -DOPENMP=ON -DGA=ON -DBUILD_SHARED_LIBS=ON -DTOOLS=ON -DFDE=ON" + + +sanity_check_paths = { + 'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.so', 'sbin/help_basis', 'pymolcas'], + 'dirs': ['data/', 'basis_library/'], +} + +modextrapaths = {'PATH': ''} + +modextravars = { + 'MOLCAS': '%(installdir)s', + 'MOLCAS_DRIVER': '%(installdir)s/pymolcas', + 'MOLCAS_SOURCE': '%(installdir)s', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/OptaDOS/OptaDOS-1.2.380-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OptaDOS/OptaDOS-1.2.380-GCC-11.3.0.eb new file mode 100644 index 000000000000..99a1e6a6a884 --- /dev/null +++ b/easybuild/easyconfigs/o/OptaDOS/OptaDOS-1.2.380-GCC-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'OptaDOS' +version = '1.2.380' + +homepage = 'http://www.optados.org/' +description = """OptaDOS is a program for calculating core-electron and low-loss electron energy +loss spectra (EELS) and optical spectra along with total-, projected- and +joint-density of electronic states (DOS) from single-particle eigenenergies and +dipole transition coefficients.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'optados-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['606d3db28dba791f62b05ef638ed0b1e42474763db65e04abd63a30501bb2eac'] + +buildopts = "SYSTEM=gfortran COMMS_ARCH=serial PREFIX=%(installdir)s " +buildopts += 'FFLAGS="$FFLAGS -fconvert=big-endian -ffree-line-length-150"' + +files_to_copy = [ + (['src/%(namelower)s.gfortran.*'], 'bin'), + 'documents', + 'examples', + 'tools', +] + +postinstallcmds = [ + "cd %(installdir)s/bin && ln -s %(namelower)s.gfortran.* %(namelower)s", +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['documents', 'examples', 'tools'] +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6-CUDA-11.7.0.eb new file mode 100644 index 000000000000..bc2f11eb6df1 --- /dev/null +++ b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6-CUDA-11.7.0.eb @@ -0,0 +1,38 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'Tarball' + +name = 'ont-guppy' +version = '6.4.6' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://community.nanoporetech.com/protocols/Guppy-protocol' +description = """ +Guppy is a bioinformatics toolkit that enables real-time basecalling and several + post-processing features that works on Oxford Nanopore Technologies™ sequencing platforms. + + For Research Use Only +""" + +toolchain = SYSTEM + +source_urls = ['https://mirror.oxfordnanoportal.com/software/analysis'] +sources = ['%(name)s_%(version)s_linux64.tar.gz'] +checksums = ['a633b2f0712781ff303a4c8fecb08d5e5603c755d6c445a6181ab11930f5bd63'] + +dependencies = [ + ('CUDA', '11.7.0'), +] + +_bins = ['guppy_%s' % x for x in ['aligner', 'barcoder', 'basecall_client', 'basecaller', 'basecaller_duplex', + 'basecaller_supervisor', 'basecall_server']] +_libs = ['lib/libvbz_hdf_plugin.a'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins] + _libs, + 'dirs': ['data'], +} + +# requires libcuda.so to be present, else it exits with code 127 +# sanity_check_commands = ['%s --help' % x for x in _bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6.eb b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6.eb new file mode 100644 index 000000000000..be0229947659 --- /dev/null +++ b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.6.eb @@ -0,0 +1,32 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'Tarball' + +name = 'ont-guppy' +version = '6.4.6' + +homepage = 'https://community.nanoporetech.com/protocols/Guppy-protocol' +description = """ +Guppy is a bioinformatics toolkit that enables real-time basecalling and several + post-processing features that works on Oxford Nanopore Technologies™ sequencing platforms. + + For Research Use Only +""" + +toolchain = SYSTEM + +source_urls = ['https://mirror.oxfordnanoportal.com/software/analysis'] +sources = ['%(name)s-cpu_%(version)s_linux64.tar.gz'] +checksums = ['5c454a1d91124ff6da1618d08cae999b0091897e7f20e3dba09038303a259bef'] + +_bins = ['guppy_%s' % x for x in ['aligner', 'barcoder', 'basecall_client', 'basecaller', 'basecaller_duplex', + 'basecaller_supervisor', 'basecall_server']] +_libs = ['lib/libvbz_hdf_plugin.a'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins] + _libs, + 'dirs': ['data'], +} + +sanity_check_commands = ['%s --help' % x for x in _bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.8-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.8-CUDA-11.7.0.eb new file mode 100644 index 000000000000..65649652d4d4 --- /dev/null +++ b/easybuild/easyconfigs/o/ont-guppy/ont-guppy-6.4.8-CUDA-11.7.0.eb @@ -0,0 +1,38 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'Tarball' + +name = 'ont-guppy' +version = '6.4.8' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://community.nanoporetech.com/protocols/Guppy-protocol' +description = """ +Guppy is a bioinformatics toolkit that enables real-time basecalling and several + post-processing features that works on Oxford Nanopore Technologies™ sequencing platforms. + + For Research Use Only +""" + +toolchain = SYSTEM + +source_urls = ['https://mirror.oxfordnanoportal.com/software/analysis'] +sources = ['%(name)s_%(version)s_linux64.tar.gz'] +checksums = ['d58aba66b1b29180946ecacf3f7b423a6933db5d12aeda783485b1ee82fd110b'] + +dependencies = [ + ('CUDA', '11.7.0'), +] + +_bins = ['guppy_%s' % x for x in ['aligner', 'barcoder', 'basecall_client', 'basecaller', 'basecaller_duplex', + 'basecaller_supervisor', 'basecall_server']] +_libs = ['lib/libvbz_hdf_plugin.a'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins] + _libs, + 'dirs': ['data'], +} + +# requires libcuda.so to be present, else it exits with code 127 +# sanity_check_commands = ['%s --help' % x for x in _bins] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb b/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb new file mode 100644 index 000000000000..b145680d1ec5 --- /dev/null +++ b/easybuild/easyconfigs/p/PALEOMIX/PALEOMIX-1.3.7-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'PALEOMIX' +version = '1.3.7' + +homepage = 'https://github.com/MikkelSchubert/paleomix' +description = """The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing + of High-Throughput Sequencing (HTS) data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SAMtools', '1.16.1'), + ('AdapterRemoval', '2.3.3'), + ('picard', '2.25.1', '-Java-11', SYSTEM), + ('Bowtie2', '2.4.5'), + ('mapDamage', '2.2.1'), + ('Pysam', '0.19.1'), + ('ruamel.yaml', '0.17.21'), +] + +use_pip = True + +exts_list = [ + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + ('ConfigArgParse', '1.5.3', { + 'checksums': ['1b0b3cbf664ab59dada57123c81eff3d9737e0d11d8cf79e3d6eb10823f1739f'], + }), + ('setproctitle', '1.3.2', { + 'checksums': ['b9fb97907c830d260fa0658ed58afd48a86b2b88aac521135c352ff7fd3477fd'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['effc402cd4207916ee062edf68b18b21b6c1adc596eea30d58805a75c8652767'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ['paleomix --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..b0f347193458 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.45' + +homepage = 'https://www.pcre.org/' + +description = """ + The PCRE library is a set of functions that implement regular expression + pattern matching using the same syntax and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'https://ftp.pcre.org/pub/pcre/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4e6ce03e0336e8b4a3d6c2b70b1c5e18590a5673a98186da90d4f33c23defc09'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +configopts = ' '.join([ + '--enable-utf', + '--enable-unicode-properties', + '--enable-pcre16', + '--enable-pcre32', +]) + +sanity_check_paths = { + 'files': ['bin/pcre-config', 'include/pcre.h', + 'share/man/man3/pcre.3', 'lib/libpcre32.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'share/doc/pcre/html', 'share/man/man1'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.42-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.42-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..01813f20f0b0 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.42-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE2' +version = '10.42' + +homepage = 'https://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c33b418e3b936ee3153de2c61cc638e7e4fe3156022a5c77d0711bcbb9d64f1f'] + +builddependencies = [('binutils', '2.40')] + +configopts = "--enable-shared --enable-jit --enable-pcre2-16 --enable-unicode" + +sanity_check_paths = { + 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "lib/libpcre2-8.a", "lib/libpcre2-16.a"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb new file mode 100644 index 000000000000..75d34f53c6c3 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.15.1-intel-2021a.eb @@ -0,0 +1,52 @@ +## +# Author: Robert Mijakovic +## +name = 'PETSc' +version = '3.15.1' + +homepage = 'https://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', + 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'PETSc_ranlib-fix.patch', + 'PETSc_remove-mpiicc-show-quotes.patch', +] +checksums = [ + {'petsc-3.15.1.tar.gz': 'c0ac6566e69d1d70b431e07e7598e9de95e84891c2452db1367c846b75109deb'}, + {'PETSc_ranlib-fix.patch': '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297'}, + {'PETSc_remove-mpiicc-show-quotes.patch': 'e6ccd7ab33d806f1e635f536d94c98b7aa36f6462d6a0f9f71b177f6ed23f09e'}, +] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Boost', '1.76.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.0'), + ('MUMPS', '5.4.0', '-metis'), + ('SuiteSparse', '5.10.1', '-METIS-5.1.0'), + ('Hypre', '2.21.0'), +] + +# enabling --with-mpi4py seems to be totally broken, leads to make errors like: +# No rule to make target 'mpi4py-build' +configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 ' + +shared_libs = 1 + +# only required when building PETSc in a SLURM job environment +# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb new file mode 100644 index 000000000000..37ddfc1c7fc7 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.18.4-intel-2021b.eb @@ -0,0 +1,47 @@ +name = 'PETSc' +version = '3.18.4' + +homepage = 'https://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', + 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'PETSc_ranlib-fix.patch', +] +checksums = [ + {'petsc-3.18.4.tar.gz': '6173d30637261c5b740c0bea14747759200ca2012c7343139f9216bc296a6394'}, + {'PETSc_ranlib-fix.patch': '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297'}, +] + +builddependencies = [('CMake', '3.22.1')] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Boost', '1.77.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.2'), + ('MUMPS', '5.4.1', '-metis'), + ('SuiteSparse', '5.10.1', '-METIS-5.1.0'), + ('Hypre', '2.24.0'), +] + +# enabling --with-mpi4py seems to be totally broken, leads to make errors like: +# No rule to make target 'mpi4py-build' +configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 ' + +shared_libs = 1 + +# only required when building PETSc in a SLURM job environment +# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch b/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch new file mode 100644 index 000000000000..0286368966ec --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc_remove-mpiicc-show-quotes.patch @@ -0,0 +1,18 @@ +The PETSc configuration script relies on the output of the command +"mpicc/mpiicc -show". For some versions of mpiicc, that command prints +include and link paths between double quotes, which confuses the PETSc +configuration script. This patch removes the double quotes again and should +only be necessary when using mpiicc newer than 2021a. +Author: Steven Vandenbrande +diff -Nru config/PETSc/Configure.py.back config/PETSc/Configure.py` +--- config/PETSc/Configure.py.back 2023-02-09 14:59:14.086680000 +0100 ++++ config/PETSc/Configure.py 2023-02-09 14:59:03.095892000 +0100 +@@ -251,7 +251,7 @@ + compiler = self.setCompilers.getCompiler() + if [s for s in ['mpicc','mpiicc'] if os.path.basename(compiler).find(s)>=0]: + try: +- output = self.executeShellCommand(compiler + ' -show', log = self.log)[0] ++ output = self.executeShellCommand(compiler + ' -show', log = self.log)[0].replace('"', '') + compiler = output.split(' ')[0] + self.addDefine('MPICC_SHOW','"'+output.strip().replace('\n','\\\\n')+'"') + except: diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..4033ffc1c52f --- /dev/null +++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-11.2.0.eb @@ -0,0 +1,61 @@ +# Contribution from Imperial College London (UK) +# Uploaded by J. Sassmannshausen + +easyblock = 'CmdCp' + +name = 'PGPLOT' +version = '5.2.2' + +homepage = 'https://sites.astro.caltech.edu/~tjp/pgplot/' +description = """The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, +device-independent graphics package for making simple scientific graphs. It is intended +for making graphical images of publication quality with minimum effort on the part of +the user. For most applications, the program can be device-independent, and the output +can be directed to the appropriate device at run time.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['ftp://ftp.astro.caltech.edu/pub/pgplot/'] +sources = ['%%(namelower)s%s.tar.gz' % version.replace('.', '')] +patches = ['PGPLOT-5.2.2_gfortran-deps-fixes.patch'] +checksums = [ + {'pgplot522.tar.gz': 'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4'}, + {'PGPLOT-5.2.2_gfortran-deps-fixes.patch': 'b1822eb32499dc18aa4aa4fae0b31c3c64ff8abb3a243716e78addafa7e58cec'}, +] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('X11', '20210802'), +] + +cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')] + +files_to_copy = [ + (['pgdemo*'], 'bin'), + (['libpgplot.*', 'libcpgplot.*'], 'lib'), + (['grfont.dat'], 'share'), + (['cpgplot.h'], 'include'), +] + +# create .so symlinks for shared libraries +postinstallcmds = [ + "cd %%(installdir)s/lib && ln -s libcpgplot.%s.5.2.2 libcpgplot.%s.5" % (SHLIB_EXT, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s libcpgplot.%s.5.2.2 libcpgplot.%s" % (SHLIB_EXT, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s libpgplot.%s.5.2.2 libpgplot.%s.5" % (SHLIB_EXT, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s libpgplot.%s.5.2.2 libpgplot.%s" % (SHLIB_EXT, SHLIB_EXT), +] + +sanity_check_paths = { + 'files': ['include/cpgplot.h', 'lib/libpgplot.a', 'lib/libcpgplot.a', + 'lib/libpgplot.%s' % SHLIB_EXT, 'lib/libcpgplot.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +modextravars = {'PGPLOT_FONT': '%(installdir)s/share/grfont.dat'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2_gfortran-deps-fixes.patch b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2_gfortran-deps-fixes.patch new file mode 100644 index 000000000000..d8073c05f6f8 --- /dev/null +++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2_gfortran-deps-fixes.patch @@ -0,0 +1,265 @@ +Patch to make sure that gfortran can be used, also includes EasyBuild specific environment variables +Some of it is based on the Debian patches +Author: J. Sassmannshausen (ICL/UK) +diff --git a/pgplot.orig/drivers/pndriv.c b/pgplot/drivers/pndriv.c +index 2b2f87d..63fa246 100644 +--- a/pgplot.orig/drivers/pndriv.c ++++ b/pgplot/drivers/pndriv.c +@@ -222,7 +222,7 @@ static void write_image_file(DeviceData *dev) { + return; + } + +- if (setjmp(png_ptr->jmpbuf)) { /* not really sure what I'm doing here... */ ++ if (setjmp(png_jmpbuf(png_ptr))) { /* not really sure what I'm doing here... */ + fprintf(stderr,"%s: error in libpng while writing file %s, plotting disabled\n", png_ident, filename); + png_destroy_write_struct(&png_ptr,&info_ptr); + dev->error = true; +diff --git a/pgplot.orig/drivers.list b/pgplot/drivers.list +index 11108bb..b6ff758 100644 +--- a/pgplot.orig/drivers.list ++++ b/pgplot/drivers.list +@@ -3,48 +3,50 @@ + ! To configure PGPLOT, ensure that drivers you do not want are + ! commented out (place ! in column 1). N.B. Many device-drivers are + ! available on selected operating systems only. ++! Modified by Gopal Narayanan for debian Jul 6, 2001 + !------------------------------------------------------------------------------ + ! File Code Description Restrictions + ! BCDRIV 0 /BCANON Canon Laser printer (bitmap version), landscape + ! CADRIV 0 /CANON Canon Laser printer, LBP-8/A2, landscape + ! CCDRIV 0 /CCP DEC LJ250 Color Companion printer +-! CGDRIV 1 /CGM CGM metafile, indexed colour selection C +-! CGDRIV 2 /CGMD CGM metafile, direct colour selection C ++ CGDRIV 1 /CGM CGM metafile, indexed colour selection C ++ CGDRIV 2 /CGMD CGM metafile, direct colour selection C + ! CWDRIV 0 /CW6320 Gould/Bryans Colourwriter 6320 pen plotter Std F77 + ! EPDRIV 0 /EPSON Epson FX100 dot matrix printer + ! EXDRIV 1 /EXCL Talaris/EXCL printers, landscape + ! EXDRIV 2 /EXCL Talaris/EXCL printers, portrait + ! GCDRIV 0 /GENICOM Genicom 4410 dot-matrix printer, landscape + ! Caution: use of GIDRIV may require a license from Unisys: +-! GIDRIV 1 /GIF GIF-format file, landscape +-! GIDRIV 2 /VGIF GIF-format file, portrait +-! GLDRIV 1 /HPGL Hewlett-Packard HP-GL plotters, landscape Std F77 +-! GLDRIV 2 /VHPGL Hewlett-Packard HP-GL plotters, portrait Std F77 ++! Since Unisys patent has expired allowing now. ++ GIDRIV 1 /GIF GIF-format file, landscape ++ GIDRIV 2 /VGIF GIF-format file, portrait ++ GLDRIV 1 /HPGL Hewlett-Packard HP-GL plotters, landscape Std F77 ++ GLDRIV 2 /VHPGL Hewlett-Packard HP-GL plotters, portrait Std F77 + ! GODRIV 0 /GOC GOC Sigma T5670 terminal VMS + ! GVDRIV 0 /GVENICOM Genicom 4410 dot-matrix printer, portrait +-! HGDRIV 0 /HPGL2 Hewlett-Packard graphics language ++ HGDRIV 0 /HPGL2 Hewlett-Packard graphics language + ! HIDRIV 0 /HIDMP Houston Instruments HIDMP pen plotter + ! HJDRIV 0 /HJ Hewlett-Packard Desk/Laserjet printer +-! HPDRIV 0 /HP7221 Hewlett-Packard HP7221 pen plotter Std F77 ++ HPDRIV 0 /HP7221 Hewlett-Packard HP7221 pen plotter Std F77 + ! LADRIV 0 /LA50 Dec LA50 and other sixel printers + ! LJDRIV 0 /LJ Hewlett-Packard LaserJet printers VMS + ! LSDRIV 1 /LIPS2 Canon LaserShot printer (landscape) + ! LSDRIV 2 /VLIPS2 Canon LaserShot printer (portrait) + ! LNDRIV 0 /LN03 Dec LN03-PLUS Laser printer (landscape) VMS + ! LVDRIV 0 /LVN03 Dec LN03-PLUS Laser printer (portrait) VMS +-! LXDRIV 0 /LATEX LaTeX picture environment ++ LXDRIV 0 /LATEX LaTeX picture environment + ! MFDRIV 0 /FILE PGPLOT graphics metafile + ! NEDRIV 0 /NEXT Computers running NeXTstep operating system + NUDRIV 0 /NULL Null device (no output) Std F77 +-! PGDRIV 0 /PGMF PGPLOT metafile (new format, experimental) Std F77 +-! PNDRIV 1 /PNG Portable Network Graphics file C +-! PNDRIV 2 /TPNG Portable Network Graphics file - transparent background C ++ PGDRIV 0 /PGMF PGPLOT metafile (new format, experimental) Std F77 ++ PNDRIV 1 /PNG Portable Network Graphics file C ++ PNDRIV 2 /TPNG Portable Network Graphics file - transparent background C + ! PPDRIV 1 /PPM Portable Pixel Map file, landscape + ! PPDRIV 2 /VPPM Portable PIxel Map file, portrait +-! PSDRIV 1 /PS PostScript printers, monochrome, landscape Std F77 +-! PSDRIV 2 /VPS Postscript printers, monochrome, portrait Std F77 +-! PSDRIV 3 /CPS PostScript printers, color, landscape Std F77 +-! PSDRIV 4 /VCPS PostScript printers, color, portrait Std F77 ++ PSDRIV 1 /PS PostScript printers, monochrome, landscape Std F77 ++ PSDRIV 2 /VPS Postscript printers, monochrome, portrait Std F77 ++ PSDRIV 3 /CPS PostScript printers, color, landscape Std F77 ++ PSDRIV 4 /VCPS PostScript printers, color, portrait Std F77 + ! PXDRIV 0 /PRINTRONI Printronix P300 or P600 dot-matrix printer + ! QMDRIV 1 /QMS QUIC devices (QMS and Talaris), landscape Std F77 + ! QMDRIV 2 /VQMS QUIC devices (QMS and Talaris), portrait Std F77 +diff --git a/pgplot.orig/makemake b/pgplot/makemake +index e48455e..93b9985 100755 +--- a/pgplot.orig/makemake ++++ b/pgplot/makemake +@@ -658,6 +658,8 @@ CPGPLOT_LIB=$CPGPLOT_LIB + # + SHARED_LIB=$SHARED_LIB + SHARED_LD=$SHARED_LD ++SHARED_LD_PGPLOT_OPTS=$SHARED_LD_PGPLOT_OPTS ++SHARED_LD_CPGPLOT_OPTS=$SHARED_LD_CPGPLOT_OPTS + # + # The libraries that the shared PGPLOT library depends upon. + # This is for systems that allow one to specify what libraries +@@ -667,6 +669,7 @@ SHARED_LD=$SHARED_LD + # libraries when they link their executables. + # + SHARED_LIB_LIBS=$SHARED_LIB_LIBS ++SHARED_LIB_CPGPLOT_LIBS=$SHARED_LIB_CPGPLOT_LIBS + # + # Ranlib command if required + # +@@ -806,7 +809,8 @@ grexec.o: grexec.f + # libraries. + #----------------------------------------------------------------------- + +-lib : libpgplot.a $(SHARED_LIB) ++#lib : libpgplot.a $(SHARED_LIB) ++lib : libpgplot.a + + libpgplot.a : $(PG_ROUTINES) $(PG_NON_STANDARD) $(GR_ROUTINES) \ + $(DISPATCH_ROUTINE) $(DRIVERS) $(SYSTEM_ROUTINES) +@@ -816,6 +820,16 @@ libpgplot.a : $(PG_ROUTINES) $(PG_NON_STANDARD) $(GR_ROUTINES) \ + $(DRIVERS) $(SYSTEM_ROUTINES) | sort | uniq` + $(RANLIB) libpgplot.a + ++#shared: $(PG_ROUTINES) $(PG_NON_STANDARD) $(GR_ROUTINES) \ ++# $(DISPATCH_ROUTINE) $(DRIVERS) $(SYSTEM_ROUTINES) ++# $(SHARED_LD) ++ ++shared: $(PG_ROUTINES) $(PG_NON_STANDARD) \ ++ $(GR_ROUTINES) $(DISPATCH_ROUTINE) $(DRIVERS) $(SYSTEM_ROUTINES) ++ $(SHARED_LD) $(SHARED_LD_PGPLOT_OPTS) `ls $(PG_ROUTINES) \ ++ $(PG_NON_STANDARD) $(GR_ROUTINES) $(DISPATCH_ROUTINE) \ ++ $(DRIVERS) $(SYSTEM_ROUTINES) | sort | uniq` $(SHARED_LIB_LIBS) ++ + EOD + + # Emit the shared library dependency if requested. +@@ -824,7 +838,7 @@ if test -n "$SHARED_LIB" -a -n "$SHARED_LD"; then + cat >> makefile << \EOD + $(SHARED_LIB): $(PG_ROUTINES) $(PG_NON_STANDARD) \ + $(GR_ROUTINES) $(DISPATCH_ROUTINE) $(DRIVERS) $(SYSTEM_ROUTINES) +- $(SHARED_LD) `ls $(PG_ROUTINES) \ ++ $(SHARED_LD) $(SHARED_LD_PGPLOT_OPTS) `ls $(PG_ROUTINES) \ + $(PG_NON_STANDARD) $(GR_ROUTINES) $(DISPATCH_ROUTINE) \ + $(DRIVERS) $(SYSTEM_ROUTINES) | sort | uniq` $(SHARED_LIB_LIBS) + EOD +@@ -1019,13 +1033,14 @@ EOD + + cat >> makefile << \EOD + ++DEB_HOST_MULTIARCH=$(shell dpkg-architecture -qDEB_HOST_MULTIARCH) ++ + # Miscellaneous include files required by drivers + + griv00.o : $(DRVDIR)/gadef.h $(DRVDIR)/gmdef.h $(DRVDIR)/gphdef.h + grivas.o : $(DRVDIR)/gadef.h + grtv00.o : $(DRVDIR)/imdef.h + pgxwin.o : $(DRVDIR)/pgxwin.h +-pndriv.o : ./png.h ./pngconf.h ./zlib.h ./zconf.h + + x2driv.o figdisp_comm.o: $(DRVDIR)/commands.h + +@@ -1039,6 +1054,8 @@ cpg: libcpgplot.a cpgplot.h cpgdemo + @echo 'will be needed.' + @echo ' ' + ++cpg-shared: libcpgplot.so ++ + pgbind: $(SRC)/cpg/pgbind.c + $(CCOMPL) $(CFLAGC) $(SRC)/cpg/pgbind.c -o pgbind + +@@ -1050,6 +1067,13 @@ libcpgplot.a cpgplot.h: $(PG_SOURCE) pgbind + $(RANLIB) libcpgplot.a + rm -f cpg*.o + ++libcpgplot.so: $(PG_SOURCE) pgbind ++ ./pgbind $(PGBIND_FLAGS) -w $(PG_SOURCE) ++ $(CCOMPL) -c $(CFLAGC) cpg*.c ++ rm -f cpg*.c ++ $(SHARED_LD) $(SHARED_LD_CPGPLOT_OPTS) cpg*.o $(SHARED_LIB_CPGPLOT_LIBS) ++ rm -f cpg*.o ++ + cpgdemo: cpgplot.h $(SRC)/cpg/cpgdemo.c libcpgplot.a + $(CCOMPL) $(CFLAGD) -c -I. $(SRC)/cpg/cpgdemo.c + $(FCOMPL) -o cpgdemo cpgdemo.o $(CPGPLOT_LIB) $(LIBS) +diff --git a/pgplot.orig/sys_linux/g77_gcc.conf b/pgplot/sys_linux/g77_gcc.conf +index d6b73e6..b3905b0 100644 +--- a/pgplot.orig/sys_linux/g77_gcc.conf ++++ b/pgplot/sys_linux/g77_gcc.conf +@@ -1,11 +1,11 @@ +-# The GNU g77 FORTRAN compiler and Gnu gcc C compiler on an elf-system. ++# The GNU gfortran FORTRAN compiler and Gnu gcc C compiler on an elf-system. + #----------------------------------------------------------------------- + + # Optional: Needed by XWDRIV (/xwindow and /xserve) and + # X2DRIV (/xdisp and /figdisp). + # The arguments needed by the C compiler to locate X-window include files. + +- XINCL="-I/usr/X11R6/include" ++ XINCL="-I${EBROOTLIBPNG}/include -I${BROOTZLIB}/include" + + # Optional: Needed by XMDRIV (/xmotif). + # The arguments needed by the C compiler to locate Motif, Xt and +@@ -34,13 +34,13 @@ + # Mandatory. + # The FORTRAN compiler to use. + +- FCOMPL="g77" ++ FCOMPL="gfortran" + + # Mandatory. + # The FORTRAN compiler flags to use when compiling the pgplot library. + # (NB. makemake prepends -c to $FFLAGC where needed) + +- FFLAGC="-u -Wall -fPIC -O" ++ FFLAGC="-u -Wall -fPIC -O3 -std=legacy " + + # Mandatory. + # The FORTRAN compiler flags to use when compiling fortran demo programs. +@@ -57,12 +57,12 @@ + # Mandatory. + # The C compiler flags to use when compiling the pgplot library. + +- CFLAGC="-Wall -fPIC -DPG_PPU -O" ++ CFLAGC="-Wall -fPIC -DPG_PPU -O3" + + # Mandatory. + # The C compiler flags to use when compiling C demo programs. + +- CFLAGD="-Wall -O" ++ CFLAGD="-Wall -O3" + + # Optional: Only needed if the cpgplot library is to be compiled. + # The flags to use when running pgbind to create the C pgplot wrapper +@@ -74,7 +74,7 @@ + # The library-specification flags to use when linking normal pgplot + # demo programs. + +- LIBS="-L/usr/X11R6/lib -lX11" ++ LIBS="-L${EBROOTLIBPNG}/lib -lpng" + + # Optional: Needed by XMDRIV (/xmotif). + # The library-specification flags to use when linking motif +@@ -108,7 +108,11 @@ + # Optional: Needed if SHARED_LIB is set. + # How to create a shared library from a trailing list of object files. + +- SHARED_LD="gcc -shared -o $SHARED_LIB" ++ SHARED_LD_PGPLOT_OPTS="-o $SHARED_LIB.5.2.2 -Wl,-soname,libpgplot.so.5.2.2" ++ ++ SHARED_LD_CPGPLOT_OPTS="-o libcpgplot.so.5.2.2 -Wl,-soname,libcpgplot.so.5.2.2" ++ ++ SHARED_LD="gfortran -shared" + + # Optional: + # On systems such as Solaris 2.x, that allow specification of the +@@ -117,7 +121,9 @@ + # library-specification flags used to specify these libraries to + # $SHARED_LD + +- SHARED_LIB_LIBS="" ++ SHARED_LIB_LIBS="-L/usr/X11R6/lib -lX11 -lpng -lc -lgfortran" ++ ++ SHARED_LIB_CPGPLOT_LIBS="-L. -lpgplot" + + # Optional: + # Compiler name used on Next systems to compile objective-C files. diff --git a/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb b/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb new file mode 100644 index 000000000000..f0929b054cd1 --- /dev/null +++ b/easybuild/easyconfigs/p/PICI-LIGGGHTS/PICI-LIGGGHTS-3.8.1-foss-2022a.eb @@ -0,0 +1,48 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'CMakeMake' + +name = 'PICI-LIGGGHTS' +version = '3.8.1' + +homepage = 'https://github.com/uob-positron-imaging-centre/PICI-LIGGGHTS' +description = """UoB Positron Imaging Centre's Improved LIGGGHTS distribution with + an emphasis on the Python interface.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/uob-positron-imaging-centre/PICI-LIGGGHTS/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['49df8c0379b00ebb57eac7c8ec25755976c2459c0a9f569090b55a0aafee628f'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('libjpeg-turbo', '2.1.3'), + ('VTK', '9.2.2'), +] + +configopts = '-DVTK_DIR=$EBROOTVTK' + +_pydir = "%(installdir)s/lib/python%(pyshortver)s/site-packages" +postinstallcmds = [ + "mkdir -p %s" % _pydir, + "cd %%(builddir)s/%%(name)s*/python && python install.py %%(installdir)s/lib %s" % _pydir, + "cp -r %(builddir)s/%(name)s*/examples %(installdir)s/", +] +start_dir = 'src' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/liggghts', 'lib/libliggghts.a', 'lib/libliggghts.%s' % SHLIB_EXT], + 'dirs': ['examples/LIGGGHTS/Tutorials_public', 'include'], +} + +sanity_check_commands = ['python -c "import liggghts"'] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/PIPITS/PIPITS-3.0-foss-2022a.eb b/easybuild/easyconfigs/p/PIPITS/PIPITS-3.0-foss-2022a.eb new file mode 100644 index 000000000000..561a7f5e9c25 --- /dev/null +++ b/easybuild/easyconfigs/p/PIPITS/PIPITS-3.0-foss-2022a.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'PIPITS' +version = '3.0' + +homepage = 'https://github.com/hsgweon/pipits' +description = """An automated pipeline for analyses of fungal internal transcribed spacer (ITS) sequences +from the Illumina sequencing platform.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), + ('VSEARCH', '2.22.1'), + ('FASTX-Toolkit', '0.0.14'), + ('ITSx', '1.1.3'), + ('HMMER', '3.3.2'), + ('RDP-Classifier', '2.13', '-Java-11', SYSTEM), + ('SeqKit', '2.3.1', '', SYSTEM), +] + +use_pip = True + +exts_list = [ + ('biom-format', '2.1.14', { + 'modulename': 'biom', + 'checksums': ['c8bac94ab6aa8226c0d38af7a3341d65e5f3664b9f45ec44fdf8b5275b2f92c1'], + }), + ('python-utils', '3.5.2', { + 'checksums': ['68198854fc276bc4b2403b261703c218e01ef564dcb072a7096ed9ea7aa5130c'], + }), + ('progressbar2', '4.2.0', { + 'modulename': 'progressbar', + 'checksums': ['1393922fcb64598944ad457569fbeb4b3ac189ef50b5adb9cef3284e87e394ce'], + }), + ('pispino', '1.1', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/hsgweon/pispino/archive/'], + 'checksums': ['8fb2e1c0ae38ecca7c637de9c0b655eb18fc67d7838ceb5a6902555ea12416c0'], + }), + (name, version, { + 'patches': ['PIPITS-3.0_remove-conda-commands.patch'], + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/hsgweon/pipits/archive/'], + 'checksums': [ + {'3.0.tar.gz': 'ee9f142e473e57b186760d940131610c16bdfe57eefca935df35779fd85377bd'}, + {'PIPITS-3.0_remove-conda-commands.patch': + 'd4be41ac4d6d37a19ad09b06c1f05ed83921aa59dc4b04b38fa257e6bce6d12f'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['pipits_funits', 'pipits_process', + 'pispino_createreadpairslist', + 'pispino_seqprep']], + 'dirs': [] +} + +sanity_check_commands = ['pipits_process --help'] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-9.2.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-9.2.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..deb26d4ed5dc --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-9.2.0-GCCcore-12.3.0.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'CMakeMake' + +name = 'PROJ' +version = '9.2.0' + +homepage = 'https://proj.org' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dea816f5aa732ae6b2ee3977b9bdb28b1d848cf56a1aad8faf6708b89f0ed50e'] + +builddependencies = [ + ('pkgconf', '1.9.5'), + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('googletest', '1.13.0'), +] + +dependencies = [ + ('SQLite', '3.42.0'), + ('LibTIFF', '4.5.0'), + ('cURL', '8.0.1'), + ('XZ', '5.4.2'), + ('nlohmann_json', '3.11.2'), +] + +# build twice, once for static, once for shared libraries +configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', + 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.309-foss-2022b.eb b/easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.309-foss-2022b.eb new file mode 100644 index 000000000000..e664b716b74a --- /dev/null +++ b/easybuild/easyconfigs/p/PYTHIA/PYTHIA-8.309-foss-2022b.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'PYTHIA' +version = '8.309' + +homepage = 'https://www.pythia.org' +description = """PYTHIA is a program for the generation of high-energy physics collision events, i.e. for the +description of collisions at high energies between electrons, protons, photons and heavy nuclei. It contains theory +and models for a number of physics aspects, including hard and soft interactions, parton distributions, initial- and +final-state parton showers, multiparton interactions, fragmentation and decay. It is largely based on original +research, but also borrows many formulae and other knowledge from the literature. As such it is categorized as a +general purpose Monte Carlo event generator.""" + + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.pythia.org/download/pythia83/'] +sources = ['pythia%(version_major)s%(version_minor)s.tgz'] +checksums = ['5bdafd9f2c4a1c47fd8a4e82fb9f0d8fcfba4de1003b8e14be4e0347436d6c33'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Python', '3.10.8'), + ('ROOT', '6.26.10'), + ('HDF5', '1.14.0'), +] + +configopts = '--cxx="$CXX" --cxx-common="$CXXFLAGS" ' +configopts += '--with-openmp --with-mpich --with-gzip --with-root --with-hdf5 ' +configopts += '--with-python --with-python-include=$EBROOTPYTHON/include/python*/ ' + +sanity_check_paths = { + 'files': ['bin/pythia%(version_major)s-config', 'lib/libpythia%(version_major)s.a', + 'lib/libpythia%%(version_major)s.%s' % SHLIB_EXT, 'lib/pythia8.%s' % SHLIB_EXT], + 'dirs': ['include/Pythia%(version_major)s', 'include/Pythia%(version_major)sPlugins', 'share'], +} +sanity_check_commands = ["python -c 'import pythia%(version_major)s'"] + +modextrapaths = {'PYTHONPATH': 'lib'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/p/Pandoc/Pandoc-3.1.2.eb b/easybuild/easyconfigs/p/Pandoc/Pandoc-3.1.2.eb new file mode 100644 index 000000000000..5916797cde83 --- /dev/null +++ b/easybuild/easyconfigs/p/Pandoc/Pandoc-3.1.2.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'Tarball' + +name = 'Pandoc' +version = '3.1.2' + +homepage = 'https://pandoc.org' +description = "If you need to convert files from one markup format into another, pandoc is your swiss-army knife" + +toolchain = SYSTEM + +_archs = {'x86_64': 'amd64', 'aarch64': 'arm64'} + +source_urls = ['https://github.com/jgm/pandoc/releases/download/%(version)s/'] +sources = ['%%(namelower)s-%%(version)s-linux-%s.tar.gz' % _archs[ARCH]] +checksums = ['4e1c607f7e4e9243fa1e1f5b208cd4f1d3f6fd055d5d8c39ba0cdc38644e1c35'] + +sanity_check_paths = { + 'files': ['bin/pandoc'], + 'dirs': ['share'], +} + +sanity_check_commands = ['pandoc --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.0-foss-2022b-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.0-foss-2022b-mpi.eb new file mode 100644 index 000000000000..8eed5565c1b5 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.0-foss-2022b-mpi.eb @@ -0,0 +1,58 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.11.0' +versionsuffix = '-mpi' + +homepage = 'https://www.paraview.org' +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["%(name)s-v%(version)s.tar.gz"] +checksums = ['68b1c6d15dd67ec442f964460c56212417e8af2a96763001f8548eb3cbc5ce87'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('XZ', '5.2.7'), + ('HDF5', '1.14.0'), + ('netCDF', '4.9.0'), + ('libGLU', '9.0.2'), + ('X11', '20221110'), + ('Mesa', '22.2.4'), + ('Qt5', '5.15.7'), + ('zlib', '1.2.12'), + ('FFmpeg', '5.1.2'), + ('Szip', '2.1.1'), +] + +# Paraview +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' +configopts += '-DPARAVIEW_USE_MPI=ON ' +configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' +configopts += '-DPARAVIEW_USE_PYTHON=ON ' +configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' + +# OpenGL & Mesa +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 1211efd9bff4..6f534c52ba2b 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -1834,6 +1834,11 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JG/JGAMBLE/'], 'checksums': ['88a20ae0736a622671b92bb2a350969af424d7610284530b277c8020235f2695'], }), + ('local::lib', '2.000029', { + 'source_tmpl': 'local-lib-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], + 'checksums': ['8df87a10c14c8e909c5b47c5701e4b8187d519e5251e87c80709b02bb33efdd7'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.3-foss-2022a.eb b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.3-foss-2022a.eb new file mode 100644 index 000000000000..3cca6b971e6a --- /dev/null +++ b/easybuild/easyconfigs/p/PhyloPhlAn/PhyloPhlAn-3.0.3-foss-2022a.eb @@ -0,0 +1,55 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO +# update to v3.0.2 + +easyblock = 'PythonPackage' + +name = 'PhyloPhlAn' +version = '3.0.3' + +homepage = 'https://github.com/biobakery/phylophlan' +description = """ +PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of +genomes and metagenomes. PhyloPhlAn is an accurate, rapid, and easy-to-use method +for large-scale microbial genome characterization and phylogenetic analysis +at multiple levels of resolution. +""" + +source_urls = ['https://github.com/biobakery/%(namelower)s/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['d8d0082c95d58d7b11a60c1e2214b35c1a23a65675005f1393e7647d76c6a054'] + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Biopython', '1.79'), + ('DendroPy', '4.5.2'), + ('matplotlib', '3.5.2'), + ('Seaborn', '0.12.1'), + ('FastTree', '2.1.11'), + ('IQ-TREE', '2.2.2.3'), + ('MUSCLE', '5.1.0'), + ('MAFFT', '7.505', '-with-extensions'), + ('SEPP', '4.5.1'), + ('trimAl', '1.4.1'), + ('BLAST+', '2.13.0'), + ('USEARCH', '11.0.667-i86linux32', '', SYSTEM), + ('DIAMOND', '2.1.0'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'phylophlan_metagenomic']], + 'dirs': ['lib'], +} +sanity_check_commands = [('%(namelower)s', '-h')] + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.20.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.20.1-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..36db893fe731 --- /dev/null +++ b/easybuild/easyconfigs/p/Pint/Pint-0.20.1-GCCcore-10.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'Pint' +version = '0.20.1' + +homepage = 'https://github.com/hgrecco/pint' +description = """Pint is a Python package to define, operate and +manipulate physical quantities: the product of a numerical value and a +unit of measurement. It allows arithmetic operations between them and +conversions from and to different units.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['387cf04078dc7dfe4a708033baad54ab61d82ab06c4ee3d4922b1e45d5626067'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-15.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-15.2-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..14b35601d98d --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-15.2-GCCcore-12.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '15.2' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['eccd208f3e7412ad7bc4c648ecc87e0aa514e02c24a48f71bf9e46910bf284ca'] + +builddependencies = [ + ('binutils', '2.39'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Perl', '5.36.0'), + ('Python', '3.10.8'), +] + +dependencies = [ + ('libreadline', '8.2'), + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = '--with-python --with-openssl' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.2.3-gompi-2021b.eb b/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.2.3-gompi-2021b.eb new file mode 100644 index 000000000000..524a8a0e657b --- /dev/null +++ b/easybuild/easyconfigs/p/Proteinortho/Proteinortho-6.2.3-gompi-2021b.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'Proteinortho' +version = '6.2.3' + +homepage = 'https://www.bioinf.uni-leipzig.de/Software/proteinortho' +description = "Proteinortho is a tool to detect orthologous genes within different species." + +toolchain = {'name': 'gompi', 'version': '2021b'} + +source_urls = ['https://gitlab.com/paulklemm_PHD/proteinortho/-/archive/v%(version)s/'] +sources = ['proteinortho-v%(version)s.tar.gz'] +checksums = ['23079b3106deb41eab4a9123ea4744e9d05ab99e286184e617628fc243718dff'] + +dependencies = [ + ('Perl', '5.34.0'), + ('Python', '3.9.6'), + ('BLAST+', '2.12.0'), + ('DIAMOND', '2.0.13'), +] + +skipsteps = ['configure'] + +preinstallopts = "mkdir -p %(installdir)s/bin && " +installopts = "PREFIX=%(installdir)s/bin" + +sanity_check_paths = { + 'files': ['bin/proteinortho', 'bin/proteinortho%(version_major)s.pl', 'bin/proteinortho_clustering'], + 'dirs': [], +} + +sanity_check_commands = ["proteinortho --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.14-gfbf-2022b.eb b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.14-gfbf-2022b.eb new file mode 100644 index 000000000000..28d542d1710e --- /dev/null +++ b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.14-gfbf-2022b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'PyGEOS' +version = '0.14' + +homepage = "https://pygeos.readthedocs.io" +description = """PyGEOS is a C/Python library with vectorized geometry functions. The geometry operations are done in + the open-source geometry library GEOS. PyGEOS wraps these operations in NumPy ufuncs providing a performance + improvement when operating on arrays of geometries.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['30fbc17f64844200b85133b885fcfb65541b8779531f6ef4f8fe467d3fba7623'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('GEOS', '3.11.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022b.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022b.eb new file mode 100644 index 000000000000..82fda5ef0753 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022b.eb @@ -0,0 +1,74 @@ +# http://www.pytables.org/usersguide/installation.html +# updated: Denis Kristak (INUITS) + +easyblock = 'PythonBundle' + +name = 'PyTables' +version = '3.8.0' + +homepage = 'https://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browsing, + processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and + disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions + such as relational or object oriented databases.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True} + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), + ('scikit-build', '0.17.2'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), # provides numexpr + ('HDF5', '1.14.0'), + ('LZO', '2.10'), + ('Blosc', '1.21.3'), + ('Blosc2', '2.8.0'), + ('py-cpuinfo', '9.0.0'), +] + +use_pip = True + +exts_list = [ + ('blosc2', '2.0.0', { + 'patches': ['blosc2-2.0.0_use-Blosc2-dep.patch'], + 'checksums': [ + {'blosc2-2.0.0.tar.gz': 'f19b0b3674f6c825b490f00d8264b0c540c2cdc11ec7e81178d38b83c57790a1'}, + {'blosc2-2.0.0_use-Blosc2-dep.patch': '6a9443f378472ada3c8fe8a8a346fe16f22b01bab7d9e60c23b64b546178054b'}, + ], + }), + ('tables', version, { + 'patches': [ + 'PyTables-%(version)s_fix-libs.patch', + 'PyTables-3.8.0_fix-find-blosc2-library-path.patch', + ], + 'checksums': [ + {'tables-3.8.0.tar.gz': '34f3fa2366ce20b18f1df573a77c1d27306ce1f2a41d9f9eff621b5192ea8788'}, + {'PyTables-3.8.0_fix-libs.patch': '7a1e6fa1f9169e52293e2b433a4302fa13c5d31e7709cd4fe0e087199b9e3f8a'}, + {'PyTables-3.8.0_fix-find-blosc2-library-path.patch': + 'dcf6c3a16a138454296161e99cf6470620755d4c26303186a744f09a11e6013b'}, + ], + }), +] + +local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb new file mode 100644 index 000000000000..d75c64e868c1 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0-CUDA-11.7.0.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Geometric' +version = '2.1.0' +local_pytorchver = '1.12.0' +versionsuffix = '-PyTorch-%s-CUDA-%%(cudaver)s' % local_pytorchver + +homepage = 'https://github.com/rusty1s/pytorch_geometric' +description = "PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('PyTorch', local_pytorchver, '-CUDA-%(cudaver)s'), + ('scikit-learn', '1.1.2'), + ('scikit-image', '0.19.3'), + ('numba', '0.56.4', '-CUDA-%(cudaver)s'), + ('h5py', '3.7.0'), + ('tqdm', '4.64.0'), + ('RDFlib', '6.2.0'), + ('ASE', '3.22.1'), + ('YACS', '0.1.8'), +] + +use_pip = True + +exts_list = [ + ('googledrivedownloader', '0.4', { + 'modulename': 'google_drive_downloader', + 'checksums': ['4b34c1337b2ff3bf2bd7581818efbdcaea7d50ffd484ccf80809688f5ca0e204'], + }), + ('plyfile', '0.7.4', { + 'checksums': ['9e9a18d22a3158fcd74df38761d43a7facc6df75126f2ab9f4e9a5d4d2188652'], + }), + ('torch_scatter', version, { + 'checksums': ['3a7124c2a033552febbdc72407f7d4d8cb6dce465720e84ab831512e81c1d208'], + }), + ('torch_sparse', '0.6.15', { + 'checksums': ['3a741ae8a7cc19247a44de549fa4d593c4257b5f741e1eb5110b712a14209dd9'], + }), + ('torch_cluster', '1.6.0', { + 'checksums': ['249c1bd8c33a887b22bf569a59d0868545804032123594dd8c76ba1885859c39'], + }), + ('torch_spline_conv', '1.2.1', { + 'checksums': ['364f658e0ecb4c5263a728c2961553e022fc44c11a633d5a1bf986cf169ab438'], + }), + ('python-louvain', '0.16', { + 'modulename': 'community.community_louvain', + 'checksums': ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'], + }), + ('torch_geometric', version, { + 'checksums': ['72653deca925885e4d613eb5c72268bb9710325d9c717516922499fbe1197079'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..17069b4ee787 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-bundle' +version = '1.12.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch.org/' +description = """PyTorch with compatible versions of official Torch extensions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.23.1'), + ('RE2', '2022-06-01'), # for torchtext +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', version, versionsuffix), + ('Pillow-SIMD', '9.2.0'), # for torchvision + ('SentencePiece', '0.1.97'), # for torchtext + ('tqdm', '4.64.0'), # for torchtext + ('double-conversion', '3.2.0'), # for torchtext + ('utf8proc', '2.7.0'), # for torchtext + ('tensorboard', '2.10.0'), # for torch-tb-profiler +] + +use_pip = True + +exts_list = [ + ('portalocker', '2.7.0', { + 'checksums': ['032e81d534a88ec1736d03f780ba073f047a06c478b06e2937486f334e955c51'], + }), + ('torchdata', '0.4.1', { + 'preinstallopts': "USE_SYSTEM_LIBS=1 ", + 'source_urls': ['https://github.com/pytorch/data/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['71c0aa3aca3b04a986a2cd4cc2e0be114984ca836dc4def2c700bf1bd1ff087e'], + }), + ('torchtext', '0.13.1', { + 'source_urls': ['https://github.com/pytorch/text/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'patches': [ + 'torchtext-0.13.1_use-system-libs.patch', + 'torchtext-0.13.1_cxx_17.patch', + ], + 'checksums': [ + {'torchtext-0.13.1.tar.gz': '1f7de1fd8c6303ea13ef2aed48a6df67df5f92d1c4a6918253be7decd93753be'}, + {'torchtext-0.13.1_use-system-libs.patch': + '3e2f170a2870ac274f452b53862f65e5e94f6da1c3af488aeb3001e0500cb0e5'}, + {'torchtext-0.13.1_cxx_17.patch': 'fd242c139baa27352d1065cece4658a3ede76f46ffec08ac04a554301e547f22'}, + ], + }), + ('torchvision', '0.13.1', { + 'source_urls': ['https://github.com/pytorch/vision/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['c32fab734e62c7744dadeb82f7510ff58cc3bca1189d17b16aa99b08afc42249'], + }), + ('pytorch-ignite', '0.4.11', { + 'modulename': 'ignite', + 'source_urls': ['https://github.com/pytorch/ignite/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['33e7485cea3cac08d7a49a3a01d3013e1156128867602bff0a8e32b2c5ebd4e9'], + }), + ('torch-tb-profiler', '0.4.1', { + 'modulename': 'torch.profiler', + 'sources': ['torch_tb_profiler-%(version)s.tar.gz'], + 'checksums': ['f2c7fb27d420be443ffde50ada655c19f76a245d21e7772de753196fd0967685'], + }), + # torchaudio-0.12.1 needs more work before it can be added +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_cxx_17.patch b/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_cxx_17.patch new file mode 100644 index 000000000000..c980e7c2ebf0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_cxx_17.patch @@ -0,0 +1,19 @@ +The error "string_view has not been declared in std" appears when not using C++17 +Split from "deps_fix" patch from torchtext +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 1ead15d46..879118c60 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -24,10 +24,10 @@ string(FIND "${CMAKE_CXX_FLAGS}" "-std=c++" env_cxx_standard) + if(env_cxx_standard GREATER -1) + message( + WARNING "C++ standard version definition detected in environment variable." +- "PyTorch requires -std=c++14. Please remove -std=c++ settings in your environment.") ++ "PyTorch requires -std=c++17. Please remove -std=c++ settings in your environment.") + endif() + +-set(CMAKE_CXX_STANDARD 14) ++set(CMAKE_CXX_STANDARD 17) + set(CMAKE_C_STANDARD 11) + + set(CMAKE_EXPORT_COMPILE_COMMANDS ON) diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_use-system-libs.patch b/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_use-system-libs.patch new file mode 100644 index 000000000000..d0902da8c9e5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-bundle/torchtext-0.13.1_use-system-libs.patch @@ -0,0 +1,67 @@ +Use external deps for third party libraries +Split from "deps_fix" patch from torchtext +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 1ead15d46..21f85e555 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -63,5 +63,9 @@ endif() + # TORCH_CXX_FLAGS contains the same -D_GLIBCXX_USE_CXX11_ABI value as PyTorch + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall ${TORCH_CXX_FLAGS}") + +-add_subdirectory(third_party) ++find_package(double-conversion) ++find_package(re2) ++find_library(SENTENCEPIECE_LIBRARY sentencepiece PATHS $ENV{EBROOTSENTENCEPIECE}/lib64) ++find_library(SENTENCEPIECE_TRAIN_LIBRARY sentencepiece_train PATHS $ENV{EBROOTSENTENCEPIECE}/lib64) ++find_library(UTF8PROC_LIBRARY utf8proc PATHS $ENV{UTF8PROC}/lib64) + add_subdirectory(torchtext/csrc) +diff --git a/packaging/build_wheel.sh b/packaging/build_wheel.sh +index 9882cb1b2..43e2a05d8 100755 +--- a/packaging/build_wheel.sh ++++ b/packaging/build_wheel.sh +@@ -10,7 +10,6 @@ setup_env + setup_wheel_python + pip_install numpy future cmake>=3.18.0 ninja + setup_pip_pytorch_version +-git submodule update --init --recursive + python setup.py clean + if [[ "$OSTYPE" == "msys" ]]; then + "$script_dir/vc_env_helper.bat" python setup.py bdist_wheel +diff --git a/setup.py b/setup.py +index 080415f7e..bd84405be 100644 +--- a/setup.py ++++ b/setup.py +@@ -68,7 +68,6 @@ class clean(distutils.command.clean.clean): + # Remove build directory + build_dirs = [ + ROOT_DIR / "build", +- ROOT_DIR / "third_party" / "build", + ] + for path in build_dirs: + if path.exists(): +diff --git a/torchtext/csrc/CMakeLists.txt b/torchtext/csrc/CMakeLists.txt +index 037f814dc..658b90342 100644 +--- a/torchtext/csrc/CMakeLists.txt ++++ b/torchtext/csrc/CMakeLists.txt +@@ -24,10 +24,6 @@ set( + set( + LIBTORCHTEXT_INCLUDE_DIRS + ${PROJECT_SOURCE_DIR} +- ${PROJECT_SOURCE_DIR}/third_party/sentencepiece/src +- $ +- $ +- $ + ${TORCH_INSTALL_PREFIX}/include + ${TORCH_INSTALL_PREFIX}/include/torch/csrc/api/include + ) +@@ -123,10 +119,6 @@ if (BUILD_TORCHTEXT_PYTHON_EXTENSION) + set( + EXTENSION_INCLUDE_DIRS + ${PROJECT_SOURCE_DIR} +- ${PROJECT_SOURCE_DIR}/third_party/sentencepiece/src +- $ +- $ +- $ + ${TORCH_INSTALL_PREFIX}/include + ${TORCH_INSTALL_PREFIX}/include/torch/csrc/api/include + ) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index 9778d40af769..855d6a9bfdd6 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -25,6 +25,7 @@ patches = [ 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -63,6 +64,8 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.11.1_skip-test_init_from_local_shards.patch '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', + # PyTorch-1.12.1_add-hypothesis-suppression.patch + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch @@ -122,6 +125,18 @@ excluded_tests = { '': [ # This test seems to take too long on NVIDIA Ampere at least. 'distributed/test_distributed_spawn', + # Produces a single test failure on some systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/fsdp/test_fsdp_core', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'test_native_mha', + # flaky test which fails on some systems, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/elastic/multiprocessing/api_test', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 + 'test_optim', ] } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index 4417c0caceea..b8fd4fe4a0b6 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -23,6 +23,7 @@ patches = [ 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -59,6 +60,8 @@ checksums = [ # PyTorch-1.11.0_increase-distributed-test-timeout.patch '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_add-hypothesis-suppression.patch + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch @@ -111,6 +114,18 @@ excluded_tests = { '': [ # This test seems to take too long on NVIDIA Ampere at least. 'distributed/test_distributed_spawn', + # Produces a single test failure on some systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/fsdp/test_fsdp_core', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'test_native_mha', + # flaky test which fails on some systems, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/elastic/multiprocessing/api_test', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 + 'test_optim', ] } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb new file mode 100644 index 000000000000..b8bf20147783 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b-CUDA-11.5.2.eb @@ -0,0 +1,173 @@ +name = 'PyTorch' +version = '1.12.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', + 'PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_python-3.10-annotation-fix.patch', + 'PyTorch-1.12.1_python-3.10-compat.patch', + 'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch', + 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.12.1_skip-failing-grad-test.patch', + 'PyTorch-1.12.1_skip-test_round_robin.patch', +] +checksums = [ + '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.11.1_skip-test_init_from_local_shards.patch + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', + # PyTorch-1.12.1_add-hypothesis-suppression.patch + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', + # PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch + 'd97cd6b0570a167ecc3e631dc4ea884d95ace285cc38aa980566f4fec2c0d089', + # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch + # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', + # PyTorch-1.12.1_fix-test_wishart_log_prob.patch + 'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45', + # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', + '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch + # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d', + 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2', # PyTorch-1.12.1_fix-vsx-vector-funcs.patch + '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2', # PyTorch-1.12.1_fix-vsx-loadu.patch + # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695', + # PyTorch-1.12.1_increase-tolerance-test_ops.patch + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb', + '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch + # PyTorch-1.12.1_python-3.10-annotation-fix.patch + '11e168fd429d9e156fc79dd806b08125f3640651ad9998abd810446b2ed0c2d7', + '81402420a878b40f824778f0333fbec6504325a6a1b06a22749c4cac3eaccf67', # PyTorch-1.12.1_python-3.10-compat.patch + # PyTorch-1.12.1_remove-flaky-test-in-testnn.patch + 'e81b678e354dd137c0d6d974605cdedbf672096fdbdf567c347bc2fbfc73471d', + # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch + # PyTorch-1.12.1_skip-test_round_robin.patch + '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349', +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.22.1'), + ('hypothesis', '6.14.6'), +] + +dependencies = [ + ('CUDA', '11.5.2', '', SYSTEM), + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.9.6'), + ('protobuf', '3.17.3'), + ('protobuf-python', '3.17.3'), + ('pybind11', '2.7.1'), + ('SciPy-bundle', '2021.10'), + ('typing-extensions', '3.10.0.2'), + ('PyYAML', '5.4.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.3.2'), + ('Pillow', '8.3.2'), + ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', SYSTEM), + ('magma', '2.6.2', '-CUDA-%(cudaver)s'), + ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), + ('expecttest', '0.1.3'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + # Broken on CUDA 11.5+(?): https://github.com/pytorch/pytorch/issues/75375 + 'distributions/test_constraints', + # Those 2 abort on some machines. Skip for now + 'distributed/fsdp/test_fsdp_input', + 'distributed/fsdp/test_fsdp_mixed_precision', + # Produces a single test failure on some systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/fsdp/test_fsdp_core', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'test_native_mha', + # flaky test which fails on some systems, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/elastic/multiprocessing/api_test', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 + 'test_optim', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +# The readelf sanity check command can be taken out once the TestRPATH test from +# https://github.com/pytorch/pytorch/pull/87593 is accepted, since it is then checked as part of the PyTorch test suite +local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT +sanity_check_commands = [ + "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, +] + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb new file mode 100644 index 000000000000..a6e1886d545c --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021b.eb @@ -0,0 +1,147 @@ +name = 'PyTorch' +version = '1.12.1' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_python-3.10-annotation-fix.patch', + 'PyTorch-1.12.1_python-3.10-compat.patch', + 'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch', + 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.12.1_skip-failing-grad-test.patch', + 'PyTorch-1.12.1_skip-test_round_robin.patch', +] +checksums = [ + '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_add-hypothesis-suppression.patch + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', + # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch + # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', + # PyTorch-1.12.1_fix-test_wishart_log_prob.patch + 'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45', + # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', + '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch + # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d', + 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2', # PyTorch-1.12.1_fix-vsx-vector-funcs.patch + '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2', # PyTorch-1.12.1_fix-vsx-loadu.patch + # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695', + # PyTorch-1.12.1_increase-tolerance-test_ops.patch + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb', + '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch + # PyTorch-1.12.1_python-3.10-annotation-fix.patch + '11e168fd429d9e156fc79dd806b08125f3640651ad9998abd810446b2ed0c2d7', + '81402420a878b40f824778f0333fbec6504325a6a1b06a22749c4cac3eaccf67', # PyTorch-1.12.1_python-3.10-compat.patch + # PyTorch-1.12.1_remove-flaky-test-in-testnn.patch + 'e81b678e354dd137c0d6d974605cdedbf672096fdbdf567c347bc2fbfc73471d', + # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch + # PyTorch-1.12.1_skip-test_round_robin.patch + '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349', +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.22.1'), + ('hypothesis', '6.14.6'), +] + +dependencies = [ + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.9.6'), + ('protobuf', '3.17.3'), + ('protobuf-python', '3.17.3'), + ('pybind11', '2.7.1'), + ('SciPy-bundle', '2021.10'), + ('typing-extensions', '3.10.0.2'), + ('PyYAML', '5.4.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.3.2'), + ('Pillow', '8.3.2'), + ('expecttest', '0.1.3'), +] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + # Produces a single test failure on some systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/fsdp/test_fsdp_core', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'test_native_mha', + # flaky test which fails on some systems, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/elastic/multiprocessing/api_test', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 + 'test_optim', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb index 528fb6715575..f7cf757ee247 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -25,6 +25,7 @@ patches = [ 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', @@ -68,6 +69,8 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.11.1_skip-test_init_from_local_shards.patch '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', + # PyTorch-1.12.1_add-hypothesis-suppression.patch + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch 'd97cd6b0570a167ecc3e631dc4ea884d95ace285cc38aa980566f4fec2c0d089', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch @@ -140,6 +143,18 @@ excluded_tests = { # Those 2 abort on some machines. Skip for now 'distributed/fsdp/test_fsdp_input', 'distributed/fsdp/test_fsdp_mixed_precision', + # Produces a single test failure on some systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/fsdp/test_fsdp_core', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'test_native_mha', + # flaky test which fails on some systems, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/elastic/multiprocessing/api_test', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 + 'test_optim', ] } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb index c31da6305720..2d70b6c97a8e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb @@ -23,6 +23,7 @@ patches = [ 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -63,6 +64,8 @@ checksums = [ # PyTorch-1.11.0_increase-distributed-test-timeout.patch '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_add-hypothesis-suppression.patch + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch @@ -123,6 +126,18 @@ excluded_tests = { 'distributed/test_distributed_spawn', # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 'distributions/test_constraints', + # Produces a single test failure on some systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/fsdp/test_fsdp_core', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'test_native_mha', + # flaky test which fails on some systems, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/17615 + 'distributed/elastic/multiprocessing/api_test', + # Fails on A10s: https://github.com/pytorch/pytorch/issues/63079 + # Fails intermittently: https://github.com/pytorch/pytorch/issues/98414 + 'test_optim', ] } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_add-hypothesis-suppression.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_add-hypothesis-suppression.patch new file mode 100644 index 000000000000..43a08b240447 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_add-hypothesis-suppression.patch @@ -0,0 +1,20 @@ +The @settings decorator overwrites `suppress_health_check` accidentally removing the `too_slow` filter +inherited by the profile. +Add it explicitely. +See https://github.com/easybuilders/easybuild-easyconfigs/issues/17615#issuecomment-1504930435 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/quantization/core/test_quantized_op.py b/test/quantization/core/test_quantized_op.py +index 41e90bc6ec7..c19324cf86a 100644 +--- a/test/quantization/core/test_quantized_op.py ++++ b/test/quantization/core/test_quantized_op.py +@@ -5569,7 +5569,7 @@ class TestQNNPackOps(TestCase): + msg="QNNPACK Sigmoid failed (FBGEMM ref)!") + + """Tests the correctness of the quantized::add (qnnpack) op.""" +- @settings(suppress_health_check=(HealthCheck.filter_too_much,)) ++ @settings(suppress_health_check=(HealthCheck.filter_too_much, HealthCheck.too_slow)) + @given(A=hu.tensor(shapes=hu.array_shapes(1, 5, 1, 5), + qparams=hu.qparams(dtypes=[torch.quint8, torch.qint8])), + zero_point=st.sampled_from([0, 2, 5, 15, 127]), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_use-predefined-data-in-test-optim.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_use-predefined-data-in-test-optim.patch new file mode 100644 index 000000000000..5dc393c17fd7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_use-predefined-data-in-test-optim.patch @@ -0,0 +1,132 @@ +The test test_optim.test_nadam has high error rate, this let's the test use +predefined data instead to be more stable. See +https://github.com/pytorch/pytorch/issues/98414 + +Viktor Rehnberg +diff --git a/test/test_optim.py b/test/test_optim.py +index 6d587b4b352..c8ec9db87e1 100644 +--- a/test/test_optim.py ++++ b/test/test_optim.py +@@ -244,8 +244,14 @@ class TestOptim(TestCase): + return set(k for k in obj.__dict__ if not k.startswith('_')) + self.assertEqual(getPublicAttr(optimizer), getPublicAttr(deepcopy(optimizer))) + +- def _test_basic_cases(self, constructor, scheduler_constructors=None, +- ignore_multidevice=False, constructor_accepts_maximize=False): ++ def _test_basic_cases( ++ self, ++ constructor, ++ scheduler_constructors=None, ++ ignore_multidevice=False, ++ constructor_accepts_maximize=False, ++ use_predefined_data=False, ++ ): + if scheduler_constructors is None: + scheduler_constructors = [] + +@@ -254,26 +260,60 @@ class TestOptim(TestCase): + return lambda weight, bias: constructor(weight, bias, maximize) + return constructor + ++ def make_weight_tensor(): ++ if use_predefined_data: ++ return torch.Tensor([ ++ [ 0.6390, -0.5524, -0.1877, -1.1132, 0.3412], ++ [-0.6489, -0.6220, -1.2537, -0.0966, 0.5481], ++ [-0.6923, 0.5768, -0.9141, 1.9410, 1.0036], ++ [ 0.5842, 1.1618, -0.1871, 1.0344, 0.5668], ++ [ 0.2123, 2.3076, 0.7522, -0.7059, 1.3849], ++ [-0.1537, 0.5159, -1.2004, 0.2017, -0.0903], ++ [ 0.9434, -0.7030, 0.0618, -1.2951, 1.7721], ++ [ 0.5890, -1.0763, -1.2541, -0.8403, -0.4343], ++ [-0.2065, -0.6883, 0.8464, -0.7792, 0.6750], ++ [-1.6577, 0.4532, 0.0791, 0.2243, 0.1148], ++ ]) ++ else: ++ return torch.randn(10, 5) ++ ++ def make_bias_tensor(): ++ if use_predefined_data: ++ return torch.Tensor([ ++ -2.4031, -0.9295, -1.0762, 0.4600, -1.8620, -0.6234, 0.1999, -0.0612, 0.8319, -1.6673, ++ ]) ++ else: ++ return torch.randn(10) ++ ++ def make_input_tensor(): ++ if use_predefined_data: ++ return torch.Tensor([1.1119, -0.4309, -0.7759, -0.0659, 0.4746]) ++ else: ++ return torch.randn(5) ++ ++ def make_non_contiguous(tensor): ++ return torch.stack([tensor, tensor]).view(*tensor.size(), 2)[..., 0] ++ + for maximize in (True, False): + self._test_state_dict( +- torch.randn(10, 5), +- torch.randn(10), +- torch.randn(5), ++ make_weight_tensor(), ++ make_bias_tensor(), ++ make_input_tensor(), + make_two_arg_constructor(constructor, maximize), + ) + self._test_basic_cases_template( +- torch.randn(10, 5), +- torch.randn(10), +- torch.randn(5), ++ make_weight_tensor(), ++ make_bias_tensor(), ++ make_input_tensor(), + constructor, + scheduler_constructors, + constructor_accepts_maximize, + ) + # non-contiguous parameters + self._test_basic_cases_template( +- torch.randn(10, 5, 2)[..., 0], +- torch.randn(10, 2)[..., 0], +- torch.randn(5), ++ make_non_contiguous(make_weight_tensor()), ++ make_non_contiguous(make_bias_tensor()), ++ make_input_tensor(), + constructor, + scheduler_constructors, + constructor_accepts_maximize, +@@ -282,9 +322,9 @@ class TestOptim(TestCase): + if not torch.cuda.is_available(): + return + self._test_basic_cases_template( +- torch.randn(10, 5).cuda(), +- torch.randn(10).cuda(), +- torch.randn(5).cuda(), ++ make_weight_tensor().cuda(), ++ make_bias_tensor().cuda(), ++ make_input_tensor().cuda(), + constructor, + scheduler_constructors, + constructor_accepts_maximize, +@@ -293,9 +333,9 @@ class TestOptim(TestCase): + if not torch.cuda.device_count() > 1 or ignore_multidevice: + return + self._test_basic_cases_template( +- torch.randn(10, 5).cuda(0), +- torch.randn(10).cuda(1), +- torch.randn(5).cuda(0), ++ make_weight_tensor().cuda(0), ++ make_bias_tensor().cuda(1), ++ make_input_tensor().cuda(0), + constructor, + scheduler_constructors, + constructor_accepts_maximize, +@@ -668,7 +708,8 @@ class TestOptim(TestCase): + self._test_basic_cases( + lambda weight, bias: optimizer( + self._build_params_dict(weight, bias, lr=1e-2), +- lr=1e-3) ++ lr=1e-3), ++ use_predefined_data=True, + ) + self._test_basic_cases( + lambda weight, bias: optimizer([weight, bias], lr=1e-3, weight_decay=0.1, momentum_decay=6e-3) diff --git a/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..721db47c2b2d --- /dev/null +++ b/easybuild/easyconfigs/p/PycURL/PycURL-7.45.2-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'PycURL' +version = '7.45.2' + +homepage = "http://pycurl.io/" +description = """PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL + from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of + features.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('cURL', '7.83.0'), +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5730590be0271364a5bddd9e245c9cc0fb710c4cbacbdd95264a3122d23224ca'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb new file mode 100644 index 000000000000..c924968a1155 --- /dev/null +++ b/easybuild/easyconfigs/p/Pyomo/Pyomo-6.5.0-foss-2022b.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'Pyomo' +version = '6.5.0' + +homepage = 'https://www.pyomo.org/' +description = """ Pyomo is a Python-based open-source software package that supports a diverse set of optimization + capabilities for formulating and analyzing optimization models. """ + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('mpi4py', '3.1.4'), +] + +exts_list = [ + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('PyUtilib', '6.0.0', { + 'checksums': ['d3c14f8ed9028a831b2bf51b8ab7776eba87e66cfc58a06b99c359aaa640f040'], + 'preinstallopts': """sed -i "s/'nose',//g" setup.py && """, + }), + (name, version, { + 'checksums': ['5a23e775bba9fdbad22698fa1a841e662482edc979f2dea41cc6c54b1bb4b968'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['pyomo -h'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb new file mode 100644 index 000000000000..0d2db0765c9d --- /dev/null +++ b/easybuild/easyconfigs/p/Python-bundle/Python-bundle-3.10.4-foss-2022a.eb @@ -0,0 +1,20 @@ +easyblock = 'Bundle' + +name = 'Python-bundle' +version = '3.10.4' + +homepage = 'https://easybuild.io/' +description = """Python distribution with a number of widely used +extensions incl. NumPy, SciPy, Matplotlib, JupyterLab, MPI4PY, ... """ + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'lowopt': True} + +dependencies = [ + ('Python', version), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('JupyterLab', '3.5.0'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..51c1ebbe912f --- /dev/null +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-3.2.12-GCCcore-11.3.0.eb @@ -0,0 +1,60 @@ +easyblock = 'CMakeMake' + +name = 'pftoolsV3' +version = '3.2.12' + +homepage = 'https://github.com/sib-swiss/pftools3' +description = """A suite of tools to build and search generalized profiles (protein and DNA).""" +software_license = 'LicenseGPLv2' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/sib-swiss/pftools3/archive/refs/tags/'] +checksums = ['1de33d6444015942afa690d54a103ad5a3d68f416fad63f247c12fa3f71a550c'] # pftools3-3.2.12.tar.gz + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('make', '4.3'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('libgd', '2.3.3'), + ('libharu', '2.3.0'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('PCRE2', '10.40'), + ('Perl', '5.34.1'), + ('zlib', '1.2.12'), +] + +configopts = '-DUSE_GRAPHICS=OFF -DUSE_PDF=ON -DUSE_AFFINITY=OFF' # Disable affinity for some old architectures + +runtest = 'test' + +sanity_check_paths = { + 'files': [ + 'bin/2ft', + 'bin/6ft', + 'bin/htop', + 'bin/pfdump', + 'bin/pfscan', + 'bin/pfscanV3', + 'bin/pfsearch', + 'bin/pfsearchV3', + 'bin/ptof', + ], + 'dirs': [ + 'share/doc', + 'share/man' + ], +} + +sanity_check_commands = [ + 'pfscanV3 --help', + 'pfsearchV3 --help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb new file mode 100644 index 000000000000..ba5ddd695731 --- /dev/null +++ b/easybuild/easyconfigs/p/phyx/phyx-1.3-foss-2022a.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'phyx' +version = '1.3' + +homepage = 'https://github.com/FePhyFoFum/%(name)s' +description = "phyx performs phylogenetics analyses on trees and sequences." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +github_account = 'FePhyFoFum' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_link_flexiblas.patch'] +checksums = [ + {'v1.3.tar.gz': 'b09677f98f997838b39cd2724463be06d0627ddc90a7e659dc90d4e02db624eb'}, + {'phyx-1.3_link_flexiblas.patch': 'e9dc98da0f3c5df8e5b8ac3e64c2b0f77358f61fc60a4aadce5ad790b636ebdd'}, +] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('Armadillo', '11.4.3'), + ('NLopt', '2.7.1'), +] + +start_dir = 'src' + +preconfigopts = "autoreconf -f -i && " + +preinstallopts = 'mkdir %(installdir)s/bin && ' + +sanity_check_paths = { + 'files': ['bin/' + _exec for _exec in ["pxaa2cdn", "pxbdfit", "pxbdsim", + "pxboot", "pxbp", "pxcat", "pxclsq", "pxcltr", "pxcolt", "pxconsq", + "pxcontrates", "pxfqfilt", "pxlog", "pxlssq", "pxlstr", "pxmrca", + "pxmrcacut", "pxmrcaname", "pxnw", "pxrecode", "pxrevcomp", + "pxrls", "pxrlt", "pxrmk", "pxrms", "pxrmt", "pxrr", "pxs2fa", "pxs2nex", + "pxs2phy", "pxseqgen", "pxssort", "pxsstat", "pxstrec", "pxsw", "pxt2new", + "pxt2nex", "pxtcol", "pxtcomb", "pxtlate", "pxtrt", "pxtscale", + "pxvcf2fa"]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/phyx/phyx-1.3_link_flexiblas.patch b/easybuild/easyconfigs/p/phyx/phyx-1.3_link_flexiblas.patch new file mode 100644 index 000000000000..1b541919cf8d --- /dev/null +++ b/easybuild/easyconfigs/p/phyx/phyx-1.3_link_flexiblas.patch @@ -0,0 +1,14 @@ +replace linking with lapack and blas by flexiblas +autor: Graham Derryberry +diff -Naur phyx-1.3.orig/src/Makefile.in phyx-1.3/src/Makefile.in +--- phyx-1.3.orig/src/Makefile.in 2023-04-12 22:44:14.000000000 -0400 ++++ phyx-1.3/src/Makefile.in 2023-04-13 09:57:34.000000000 -0400 +@@ -17,7 +17,7 @@ + HARM := @HARM@ + HOMP := @HOMP@ + +-CPP_LIBS = -llapack -lblas -lpthread -lm ++CPP_LIBS = -lflexiblas -lpthread -lm + ifeq "$(HNLOPT)" "Y" + CPP_LIBS += -lnlopt + endif diff --git a/easybuild/easyconfigs/p/picard/picard-3.0.0-Java-17.eb b/easybuild/easyconfigs/p/picard/picard-3.0.0-Java-17.eb new file mode 100644 index 000000000000..b9cd29fae762 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-3.0.0-Java-17.eb @@ -0,0 +1,60 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: MIT +# +# 2.10.1: +# Adam Huffman +# The Francis Crick Institute +# 2.18.11: +# Jonas Demeulemeester +# The Francis Crick Institute +# 2.21.1 +# Pavel Grochal (INUITS) +# 2.25.1 +# J. Sassmannshausen (GSTT) +# 2.25.5 +# Erica Bianco (HPCNow!) +# 2.26.10 +# Christoph Siegert (Leipzig University) +# 3.0.0 +# Graham Derryberry (UTK) +## + +easyblock = 'JAR' + +name = 'picard' +version = '3.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://broadinstitute.github.io/picard/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] +sources = [{ + 'filename': '%(name)s-%(version)s.jar', + 'download_filename': '%(name)s.jar', +}] +checksums = ['0d5e28ab301fad3b02030d01923888129ba82c5f722ac5ccb2d418ab76ac5499'] + +postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"] + +dependencies = [('Java', '17')] + +sanity_check_commands = ['java -jar $EBROOTPICARD/picard.jar 2>&1 | grep USAGE'] + +sanity_check_paths = { + 'files': ['picard.jar'], + 'dirs': [], +} + +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..6e817cde0bd6 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.4-GCCcore-13.1.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '1.9.4' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = ['https://distfiles.dereferenced.org/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d6b844ab6bf8ca685e9ef8103dee64fb39b2484c7a18da64ae5ba269514c9f78'] + +builddependencies = [('binutils', '2.40')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..716412bd025d --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconf/pkgconf-1.9.5-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'pkgconf' +version = '1.9.5' + +homepage = 'https://github.com/pkgconf/pkgconf' + +description = """pkgconf is a program which helps to configure compiler and linker flags for development libraries. + It is similar to pkg-config from freedesktop.org.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://distfiles.dereferenced.org/pkgconf/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6466efd2e38c4c0ac5de4e345f0dc6dad57e689efb08c31f2a71547683d20dc7'] + +builddependencies = [('binutils', '2.40')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s pkgconf pkg-config"] + +sanity_check_paths = { + 'files': ['bin/pkg-config', 'bin/pkgconf'], + 'dirs': [], +} + +sanity_check_commands = [ + "pkg-config --help", + "pkgconf --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb new file mode 100644 index 000000000000..e1c12919d470 --- /dev/null +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8-foss-2022a.eb @@ -0,0 +1,86 @@ +easyblock = 'CMakeMake' + +name = 'pod5-file-format' +version = '0.1.8' + +homepage = 'https://github.com/nanoporetech/pod5-file-format' +description = """POD5 is a file format for storing nanopore dna data in an easily accessible way. + The format is able to be written in a streaming manner which allows a sequencing + instrument to directly write the format.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/nanoporetech/%(name)s/archive/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['pod5-file-format-0.1.8_dep_fix.patch'] +checksums = [ + {'pod5-file-format-0.1.8.tar.gz': '262b85a44b2e5e93be55bfc2d55a49c07a012b04b59aa24e1d59fd981ac58b5c'}, + {'pod5-file-format-0.1.8_dep_fix.patch': '9c7fe8e8aa79c8fff9e43ea3ae1754c5ef0d3023c47f7e4a157d12b34be378a4'}, +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('pkgconfig', '1.5.5', '-python'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Arrow', '8.0.0'), + ('SciPy-bundle', '2022.05'), + ('zstd', '1.5.2'), + ('flatbuffers', '2.0.7'), + ('pybind11', '2.9.2'), + ('Boost', '1.79.0'), + ('build', '0.10.0'), + ('HDF5', '1.12.2'), + ('h5py', '3.7.0'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, + 'installopts': '', +} + +exts_list = [ + ('attrs', '22.2.0', { + 'checksums': ['c9227bfc2f01993c03f68db37d1d15c9690188323c067c641f1a35ca58185f99'], + }), + ('vbz_h5py_plugin', '1.0.1', { + 'checksums': ['c784458bb0aad6303474cb2f10956179116b35555803fd1154eb4ef362519341'], + }), + ('iso8601', '1.1.0', { + 'checksums': ['32811e7b81deee2063ea6d2e94f8819a86d1f3811e49d23623a41fa832bef03f'], + }), + ('pod5', version, { + 'source_urls': source_urls, + 'sources': sources, + 'start_dir': 'python/pod5', + 'checksums': ['262b85a44b2e5e93be55bfc2d55a49c07a012b04b59aa24e1d59fd981ac58b5c'], + }), +] + +configopts = ' -DBUILD_PYTHON_WHEEL=ON -DZSTD_LIB="$EBROOTZSTD/lib/libzstd.a" ' + +installopts = ' && export XDG_CACHE_HOME=%(builddir)s && cd %(installdir)s' +installopts += ' && pip install --no-deps --ignore-installed --prefix %(installdir)s lib_pod5-%(version)s-*.whl' + +postinstallcmds = ['rm %(installdir)s/lib_pod5-%(version)s-*.whl'] + +sanity_check_paths = { + 'files': ['bin/pod5', 'lib/libpod5_format.a'], + 'dirs': ['include/pod5_format', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "pod5 subset --help", + "python -c 'import lib_pod5'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch new file mode 100644 index 000000000000..3015c600bb5b --- /dev/null +++ b/easybuild/easyconfigs/p/pod5-file-format/pod5-file-format-0.1.8_dep_fix.patch @@ -0,0 +1,31 @@ +Flatbuffers 2.0.7 uses capital 'B' in 'FlatBuffersConfig.cmake' +We want to use our pybind11 instead of the one in git submodules +Author: Petr Král (INUITS) +diff -u pod5-file-format-0.1.8/c++/CMakeLists.txt.orig pod5-file-format-0.1.8/c++/CMakeLists.txt +--- pod5-file-format-0.1.8/c++/CMakeLists.txt.orig 2023-02-23 19:17:13.000000000 +0100 ++++ pod5-file-format-0.1.8/c++/CMakeLists.txt 2023-04-25 14:07:28.174884834 +0200 +@@ -16,11 +16,12 @@ + COMPONENTS + headers + ) +- find_package(Flatbuffers REQUIRED) ++ find_package(FlatBuffers REQUIRED) + find_package(zstd REQUIRED) + endif() + + find_package(Threads REQUIRED) ++find_package(pybind11 REQUIRED) + + find_program( + FLATBUFFERS_FLATC_EXECUTABLE +diff -u pod5-file-format-0.1.8/CMakeLists.txt.orig pod5-file-format-0.1.8/CMakeLists.txt +--- pod5-file-format-0.1.8/CMakeLists.txt.orig 2023-01-20 12:22:05.000000000 +0100 ++++ pod5-file-format-0.1.8/CMakeLists.txt 2023-01-23 10:34:44.860294168 +0100 +@@ -92,7 +91,6 @@ + + if (BUILD_PYTHON_WHEEL) + find_package (Python ${PYTHON_VERSION} EXACT COMPONENTS Interpreter Development) +- add_subdirectory(third_party/pybind11) + endif() + + add_subdirectory(c++) diff --git a/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2021b.eb b/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2021b.eb new file mode 100644 index 000000000000..a15d42eeece5 --- /dev/null +++ b/easybuild/easyconfigs/p/polymake/polymake-4.8-foss-2021b.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'polymake' +version = '4.8' + +homepage = 'https://polymake.org' +description = """polymake is open source software for research in polyhedral geometry. +It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, +graphs, tropical hypersurfaces, and other objects.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://polymake.org/lib/exe/fetch.php/download/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['3f7bd19d6ac1372ae32368e57134ff37a11fbe9eb1f6abe8195b34c5eec29b11'] + +dependencies = [ + ('Ninja', '1.10.2'), + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), + ('libreadline', '8.1'), + ('Perl', '5.34.0'), + ('SVG', '2.87'), + ('GMP', '6.2.1'), + ('MPFR', '4.1.0'), + ('Boost', '1.77.0'), + ('FLINT', '2.8.4'), + ('Java', '11', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/polymake', 'bin/polymake-config', 'lib/libpolymake.%s' % SHLIB_EXT, + 'lib/libpolymake-apps.%s' % SHLIB_EXT, 'lib/libpolymake-apps-rt.%s' % SHLIB_EXT], + 'dirs': ['include/polymake', 'lib/polymake', 'share/polymake'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/polymake/polymake-4.8-GCC-11.3.0.eb b/easybuild/easyconfigs/p/polymake/polymake-4.8-gfbf-2022a.eb similarity index 95% rename from easybuild/easyconfigs/p/polymake/polymake-4.8-GCC-11.3.0.eb rename to easybuild/easyconfigs/p/polymake/polymake-4.8-gfbf-2022a.eb index bb766d019559..5eff12ad133b 100644 --- a/easybuild/easyconfigs/p/polymake/polymake-4.8-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/polymake/polymake-4.8-gfbf-2022a.eb @@ -8,7 +8,7 @@ description = """polymake is open source software for research in polyhedral geo It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, graphs, tropical hypersurfaces, and other objects.""" -toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchain = {'name': 'gfbf', 'version': '2022a'} source_urls = ['https://polymake.org/lib/exe/fetch.php/download/'] sources = [SOURCE_TAR_BZ2] diff --git a/easybuild/easyconfigs/p/powerlaw/powerlaw-1.5-foss-2022a.eb b/easybuild/easyconfigs/p/powerlaw/powerlaw-1.5-foss-2022a.eb new file mode 100644 index 000000000000..76d531749152 --- /dev/null +++ b/easybuild/easyconfigs/p/powerlaw/powerlaw-1.5-foss-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'powerlaw' +version = '1.5' + +homepage = 'http://www.github.com/jeffalstott/powerlaw' +description = "powerlaw: A Python Package for Analysis of Heavy-Tailed Distributions" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_PY3_WHL] +checksums = ['633a669573d9fd663d2f452f121117f2d6b2f2c502eca532f9355f733abfec96'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb b/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb new file mode 100644 index 000000000000..ee3db5ffcf26 --- /dev/null +++ b/easybuild/easyconfigs/p/pp-sketchlib/pp-sketchlib-2.1.1-foss-2022a.eb @@ -0,0 +1,44 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'pp-sketchlib' +version = '2.1.1' + +homepage = 'https://github.com/bacpop/pp-sketchlib' +description = """Library of sketching functions used by PopPUNK""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), + ('HDF5', '1.12.2'), + ('pybind11', '2.9.2'), + ('Eigen', '3.4.0'), + ('Boost', '1.79.0'), + ('nlohmann_json', '3.10.5'), + ('HighFive', '2.6.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + (name, version, { + 'source_urls': ['https://github.com/bacpop/pp-sketchlib/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['b42acf0a58ea3225e3fe95adc8fc165578832c58e6f5b6fb3f7817655e0a9f30'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022a.eb new file mode 100644 index 000000000000..c1a3cfa1cd2f --- /dev/null +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2022a.eb @@ -0,0 +1,50 @@ +# EasyBuild easyconfig +# +# John Dey jfdey@fredhutch.org +# Fred Hutchenson Cancer Research Center +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'Tarball' + +name = 'prokka' +version = '1.14.5' + +homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml' +description = "Prokka is a software tool for the rapid annotation of prokaryotic genomes." + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/tseemann/prokka/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] + +dependencies = [ + ('BioPerl', '1.7.8'), + ('BLAST+', '2.13.0'), + ('Java', '11', '', SYSTEM), + ('Bio-SearchIO-hmmer', '1.7.3'), + ('parallel', '20220722'), + ('tbl2asn', '20220427', '-linux64', SYSTEM), +] + +local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', + 'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm', + 'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db', + 'prokka-make_tarball'] + +postinstallcmds = ["%(installdir)s/bin/prokka --setupdb"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'], + 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], +} + +sanity_check_commands = [ + "prokka --version", + "prokka --listdb", +] + +modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..5a00b1b6fddc --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.23.0-GCCcore-12.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '4.23.0' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] +sources = ['protobuf-%(version)s.tar.gz'] +checksums = ['5f1eba1da2a2f3f7df469fccddef3cc060b8a16cfe3cc65961ad36b4dbcf59c5'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('protobuf', '23.0') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Make sure protobuf is installed as a regular folder or it will not be found if +# other google packages are installed in other site-packages folders +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'], +} + +options = {'modulename': 'google.protobuf'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-23.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-23.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..962f6810124c --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-23.0-GCCcore-12.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'protobuf' +version = '23.0' + +homepage = 'https://github.com/protocolbuffers/protobuf' +description = """Protocol Buffers (a.k.a., protobuf) are Google's +language-neutral, platform-neutral, extensible mechanism for +serializing structured data.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/protocolbuffers/protobuf/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b8faf8487cc364e5c2b47a9abd77512bc79a6389ea45392ca938ba7617eae877'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +srcdir = '.' + +configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON -Dprotobuf_ABSL_PROVIDER="package" ' + +dependencies = [ + ('Abseil', '20230125.2'), +] + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..a36d83f17ab7 --- /dev/null +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'py-cpuinfo' +version = '9.0.0' + +homepage = 'https://github.com/workhorsy/py-cpuinfo' +description = "py-cpuinfo gets CPU info with pure Python." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/cpuinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cpuinfo", + "python -m cpuinfo", +] + +options = {'modulename': 'cpuinfo'} + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..9e22b8a26a6b --- /dev/null +++ b/easybuild/easyconfigs/p/py3Dmol/py3Dmol-2.0.1.post1-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'py3Dmol' +version = '2.0.1.post1' + +homepage = 'https://github.com/3dmol/3Dmol.js/tree/master/py3Dmol' +description = "A simple IPython/Jupyter widget to embed an interactive 3Dmol.js viewer in a notebook." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': '%(name)s', + 'checksums': ['add70ecf8f647970925eb8c1043c5c1343813fa49e613b77f0628e522c4148ac'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.13.1-foss-2022a.eb new file mode 100755 index 000000000000..fa32aafe1c26 --- /dev/null +++ b/easybuild/easyconfigs/p/pyFFTW/pyFFTW-0.13.1-foss-2022a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'pyFFTW' +version = '0.13.1' + +homepage = 'https://github.com/pyFFTW/pyFFTW' +description = """A pythonic wrapper around FFTW, the FFT library, presenting a unified interface + for all the supported transforms.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['09155e90a0c6d0c1f2d1f3668180a7de95fb9f83fef5137a112fb05978e87320'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..796120e325ec --- /dev/null +++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.4-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'pydantic' +version = '1.10.4' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('typing_extensions', '4.4.0', { + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + (name, version, { + 'checksums': ['b9a3859f24eb4e097502a3be1fb4b2abb79b6103dd9e2e0edb70613a4459a648'], + }), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..c0f68a2a026d --- /dev/null +++ b/easybuild/easyconfigs/p/pydot/pydot-1.4.2-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'PythonPackage' + +name = 'pydot' +version = '1.4.2' + +homepage = 'https://github.com/pydot/pydot' +description = "Python interface to Graphviz's Dot language." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['248081a39bcb56784deb018977e428605c1c758f10897a339fce1dd728ff007d'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('Graphviz', '2.50.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb new file mode 100644 index 000000000000..bc8ccfc43a97 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.3.10-foss-2022a.eb @@ -0,0 +1,81 @@ +easyblock = 'PythonBundle' + +name = 'pymatgen' +version = '2023.3.10' + +homepage = 'https://pymatgen.org/' +description = """Python Materials Genomics is a robust materials analysis code that defines core object + representations for structures and molecules with support for many electronic structure codes.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('hypothesis', '6.46.7'), # required for numpy tests +] + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('matplotlib', '3.5.2'), + ('networkx', '2.8.4'), + ('sympy', '1.10.1'), + ('plotly.py', '5.12.0'), + ('tqdm', '4.64.0'), + +] + +use_pip = True + +# pymatgen 2023.3.10 requires spglib >= 2.0.2 +# skip import check for ruamel.yaml.clib, covered by import check for ruamel.yaml extension +exts_list = [ + ('monty', '2022.9.9', { + 'checksums': ['6cca8f14a18a2030b243a1377dfd59049a1ccce007b34f810a8f5eece72b9ceb'], + }), + ('palettable', '3.3.0', { + 'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'], + }), + ('ruamel.yaml.clib', '0.2.7', { + 'modulename': False, + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + }), + ('ruamel.yaml', '0.17.21', { + 'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'], + }), + ('uncertainties', '3.1.7', { + 'checksums': ['80111e0839f239c5b233cb4772017b483a0b7a1573a581b92ab7746a35e6faab'], + }), + ('latexcodec', '2.0.1', { + 'checksums': ['2aa2551c373261cefe2ad3a8953a6d6533e68238d180eb4bb91d7964adb3fe9a'], + }), + ('pybtex', '0.24.0', { + 'checksums': ['818eae35b61733e5c007c3fcd2cfb75ed1bc8b4173c1f70b56cc4c0802d34755'], + }), + ('pydantic', '1.10.2', { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), + ('emmet-core', '0.49.1', { + 'modulename': 'emmet', + 'checksums': ['8133d63900c170ac5c66efe8d70c32c9762c9a42fc150a79c7c90a8477ac81ec'], + }), + ('mp-api', '0.30.10', { + 'checksums': ['b58522b106f362d6917eba97ef8d699cc87210b65a9f0a8ac70c0841110ce50a'], + }), + ('spglib', '2.0.2', { + 'checksums': ['1d081ec22da4ab4fc3198e9445ddad6dec2261c43927831151d93e39422610aa'], + }), + (name, version, { + 'checksums': ['20a5d1681e2951d2710d5358197b5b58992e2b0ec4217a5ba966cf28513c1283'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pmg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pmg --help"] + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..5accb085ce1e --- /dev/null +++ b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.0.9-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'pyparsing' +version = '3.0.9' + +homepage = 'https://github.com/pyparsing/pyparsing' +description = """The pyparsing module is an alternative approach to creating and +executing simple grammars, vs. the traditional lex/yacc approach, or the use of +regular expressions. The pyparsing module provides a library of classes that +client code uses to construct the grammar directly in Python code.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pyperf/pyperf-2.6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pyperf/pyperf-2.6.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..2cc5f691e4ae --- /dev/null +++ b/easybuild/easyconfigs/p/pyperf/pyperf-2.6.0-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'pyperf' +version = '2.6.0' + +homepage = 'https://github.com/psf/pyperf' +description = "The Python pyperf module is a toolkit to write, run and analyze benchmarks" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d7e367a1ec7035d7a2b25f55a5925596c00cb15851f28cffd85b05b7307232af'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/pyperf'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyperf --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-3.5.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-3.5.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..f90f4e9a5b12 --- /dev/null +++ b/easybuild/easyconfigs/p/pyproj/pyproj-3.5.0-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'pyproj' +version = '3.5.0' + +homepage = 'https://pyproj4.github.io/pyproj' +description = "Python interface to PROJ4 library for cartographic transformations" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9859d1591c1863414d875ae0759e72c2cffc01ab989dc64137fbac572cc81bf6'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('PROJ', '9.1.1'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " + +sanity_check_paths = { + 'files': ['bin/pyproj'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['pyproj --help'] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pyslim/pyslim-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/p/pyslim/pyslim-1.0.1-foss-2022a.eb new file mode 100644 index 000000000000..da7c91bba128 --- /dev/null +++ b/easybuild/easyconfigs/p/pyslim/pyslim-1.0.1-foss-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'pyslim' +version = '1.0.1' + +homepage = 'https://tskit.dev/pyslim/docs/stable/introduction.html' +description = """A Python API for reading and modifying tskit tree +sequence files produced by SLiM, or modifying files produced by other +programs (e.g., msprime, fwdpy11, and tsinfer) for use in SLiM.""" + + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # for numpy + ('msprime', '1.2.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['d65923658df9303962997f8911449245d33cf7f56aada8df4573ad301a9934c6'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..3f3e9090b618 --- /dev/null +++ b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'pytesseract' +version = '0.3.10' + +homepage = "https://github.com/madmaze/pytesseract" +description = """Python-tesseract is an optical character recognition (OCR) +tool for python. That is, it will recognize and "read" the text embedded in +images. + +Python-tesseract is a wrapper for Google's Tesseract-OCR Engine. It is also +useful as a stand-alone invocation script to tesseract, as it can read all +image types supported by the Pillow and Leptonica imaging libraries, including +jpeg, png, gif, bmp, tiff, and others. Additionally, if used as a script, +Python-tesseract will print the recognized text instead of writing it to a +file.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +patches = ['pytesseract-0.3.10_relax-packaging-version-requirements.patch'] +checksums = [ + {SOURCELOWER_TAR_GZ: 'f1c3a8b0f07fd01a1085d451f5b8315be6eec1d5577a6796d46dc7a62bd4120f'}, + {'pytesseract-0.3.10_relax-packaging-version-requirements.patch': + '17bcf10055dd421572654b8da3a7899115c0eb50ec32bb6ab58371d16530f8c6'}, +] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('tesseract', '5.3.0'), + ('Python', '3.10.4'), + ('Pillow', '9.1.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10_relax-packaging-version-requirements.patch b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10_relax-packaging-version-requirements.patch new file mode 100644 index 000000000000..90471c982798 --- /dev/null +++ b/easybuild/easyconfigs/p/pytesseract/pytesseract-0.3.10_relax-packaging-version-requirements.patch @@ -0,0 +1,14 @@ +Packaging is used with Version, parse and InvalidVersion that does not strictly +need the versions specified in setup.cfg +Author: Viktor Rehnberg +--- ./setup.cfg.orig 2023-05-11 10:30:41.231633193 +0200 ++++ ./setup.cfg 2023-05-11 10:33:01.127272708 +0200 +@@ -27,7 +27,7 @@ + packages = find: + include_package_data = True + install_requires = +- packaging>=21.3 ++ packaging>=20.9 + Pillow>=8.0.0 + python_requires = >=3.7 + diff --git a/easybuild/easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb new file mode 100755 index 000000000000..f5d720e5b7a9 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'pytest-cpp' +version = '2.3.0' + +homepage = 'http://github.com/pytest-dev/pytest-cpp' +description = """Use pytest runner to discover and execute C++ tests.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] +dependencies = [('Python', '3.10.4')] + +use_pip = True +sanity_pip_check = True +download_dep_fail = False + +sources = [SOURCE_TAR_GZ] +checksums = ['37abfa693697940aed2e7c034698188dee3616183ad9b3f764f3b06aeb75ed4a'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb new file mode 100755 index 000000000000..af5753f1645a --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,21 @@ +easyblock = 'PythonPackage' + +name = 'pytest-flakefinder' +version = '1.1.0' + +homepage = 'https://github.com/dropbox/pytest-flakefinder' +description = """Runs tests multiple times to expose flakiness.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] +dependencies = [('Python', '3.10.4')] + +use_pip = True +sanity_pip_check = True +download_dep_fail = False + +sources = [SOURCE_TAR_GZ] +checksums = ['e2412a1920bdb8e7908783b20b3d57e9dad590cc39a93e8596ffdd493b403e0e'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..8f1d64d75285 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-7.2.2-GCCcore-11.2.0.eb @@ -0,0 +1,80 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '7.2.2' + +homepage = 'https://docs.pytest.org/en/latest/' +description = """The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# Note! Some of the file system related tests may fail on shared file systems. +# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir +# and test_source_mtime_long_long are known to fail on GPFS +# Build with buildpath and tmpdir set to a local file system to avoid this +# or use --ignore-test-failures +_skip_tests = [ + 'testing/io/test_terminalwriter.py', + 'testing/test_terminal.py', + 'testing/test_debugging.py', + 'testing/test_config.py', + 'testing/test_helpconfig.py', +] +_ignore_tests = ' --ignore='.join(_skip_tests) + +exts_list = [ + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('setuptools-scm', '7.1.0', { + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], + }), + ('flit-core', '3.8.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + 'checksums': ['b305b30c99526df5e63d6022dd2310a0a941a187bd3884f4c8ef0418df6c39f3'], + }), + ('flit-scm', '1.7.0', { + 'source_tmpl': 'flit_scm-%(version)s.tar.gz', + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('exceptiongroup', '1.1.0', { + 'checksums': ['bcb67d800a4497e1b404c2dd44fca47d3b7a5e5433dbab67f96c1a685cdfdf23'], + }), + ('hypothesis', '6.54.6', { + 'checksums': ['2d5e2d5ccd0efce4e0968a6164f4e4853f808e33f4d91490c975c98beec0c7c3'], + }), + ('elementpath', '4.0.1', { + 'checksums': ['1162e4c8e5501bd36291b668f4449b8125fea5ef64a26da8d71da31126725aa5'], + }), + ('xmlschema', '2.2.2', { + 'checksums': ['0caa96668807b4b51c42a0fe2b6610752bc59f069615df3e34dcfffb962973fd'], + }), + (name, version, { + 'checksums': ['c99ab0c73aceb050f68929bc93af19ab6db0558791c6a0715723abe9d0ade9d4'], + }), +] + +sanity_check_commands = [ + "python -c 'import pytest'", + 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' + % _ignore_tests, +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..4dc389d5dc9e --- /dev/null +++ b/easybuild/easyconfigs/p/python-docx/python-docx-0.8.11-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'python-docx' +version = '0.8.11' + +homepage = 'https://python-docx.readthedocs.io/en/latest/' +description = 'python-docx is a Python library for creating and updating Microsoft Word (.docx) files' + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1105d233a0956dd8dd1e710d20b159e2d72ac3c301041b95f4d4ceb3e0ebebc4'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('lxml', '4.9.2'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +options = {'modulename': 'docx'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.2.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.2.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..54e733c36c8c --- /dev/null +++ b/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.2.0-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'python-xxhash' +version = '3.2.0' + +homepage = 'https://github.com/ifduyue/python-xxhash' +description = 'xxhash is a Python binding for the xxHash library by Yann Collet.' + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('xxHash', '0.8.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xxhash', version, { + 'checksums': ['1afd47af8955c5db730f630ad53ae798cf7fae0acb64cebb3cf94d35c47dd088'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.4.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..4ca3e9f8a2ea --- /dev/null +++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.4.0-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Qtconsole' +version = '5.4.0' + +homepage = 'https://jupyter.org/' +description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media +output, session export, and more. +The Qtconsole is a very lightweight application that largely feels like a +terminal, but provides a number of enhancements only possible in a GUI, such as +inline figures, proper multiline editing with syntax highlighting, graphical +calltips, and more.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['57748ea2fd26320a0b77adba20131cfbb13818c7c96d83fafcb110ff55f58b35'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), + ('QtPy', '2.3.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb index 9257514652d9..87066c6ae6d7 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb @@ -11,20 +11,20 @@ It is based on density-functional theory, plane waves, and pseudopotentials toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'usempi': True, 'openmp': True} -source_urls = [ - 'https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s', -] sources = [ { 'filename': 'q-e-qe-%(version)s.tar.gz', 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', + 'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s'], }, { 'filename': 'qe-gipaw-%(version)s.tar.gz', 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/'] }, - {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', - 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']}, + { + 'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'] + }, ] checksums = [ 'd56dea096635808843bd5a9be2dee3d1f60407c01dbeeda03f8256a3bcfc4eb6', # q-e-qe-7.1.tar.gz diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb index e9f900390052..a81be226c253 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb @@ -11,20 +11,20 @@ It is based on density-functional theory, plane waves, and pseudopotentials toolchain = {'name': 'intel', 'version': '2022a'} toolchainopts = {'usempi': True, 'openmp': True} -source_urls = [ - 'https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s', -] sources = [ { 'filename': 'q-e-qe-%(version)s.tar.gz', 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', + 'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s'], }, { 'filename': 'qe-gipaw-%(version)s.tar.gz', 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/'] }, - {'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', - 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/']}, + { + 'filename': 'wannier90-3.1.0.tar.gz', 'download_filename': 'v3.1.0.tar.gz', + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'] + }, ] checksums = [ 'd56dea096635808843bd5a9be2dee3d1f60407c01dbeeda03f8256a3bcfc4eb6', # q-e-qe-7.1.tar.gz diff --git a/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022a.eb b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022a.eb new file mode 100644 index 000000000000..1b0932b22af0 --- /dev/null +++ b/easybuild/easyconfigs/q/qnorm/qnorm-0.8.1-foss-2022a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'qnorm' +version = '0.8.1' + +homepage = 'https://github.com/Maarten-vd-Sande/qnorm' +description = "Fast-ish (and correct!) quantile normalization in Python" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('numba', '0.56.4'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['61b2f3ef09a9c552a4f3b83dc438cb13f191fa190164361a3a508c4777eed3c7'] + +download_dep_fail = True +use_pip = True + +# pyproject.toml included in qnorm source tarball does not include standard fields, +# it's only there to be read by setup.py... +preinstallopts = "sed -i 's/pyproject.toml/pyproject.toml_/g' setup.py && mv pyproject.toml pyproject.toml_ && " + +sanity_check_paths = { + 'files': ['bin/qnorm'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["qnorm --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/R-MXM/R-MXM-1.5.5-foss-2021b.eb b/easybuild/easyconfigs/r/R-MXM/R-MXM-1.5.5-foss-2021b.eb new file mode 100644 index 000000000000..fbbc6f6be34c --- /dev/null +++ b/easybuild/easyconfigs/r/R-MXM/R-MXM-1.5.5-foss-2021b.eb @@ -0,0 +1,54 @@ +easyblock = 'Bundle' + +name = 'R-MXM' +version = '1.5.5' + +homepage = 'https://cran.r-project.org/package=MXM' +description = "MXM: Feature Selection (Including Multiple Solutions) and Bayesian Networks" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('R', '4.1.2'), +] + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_list = [ + ('sets', '1.0-24', { + 'checksums': ['e75733f5c9418eb09fb950a4a94ccf84ddd88231c61ee80d02b7f0917debcac9'], + }), + ('relations', '0.6-13', { + 'checksums': ['f859c336fb0c4a2df7f294b33d1d04f95c6988e5e76933e2e70bf291d904d9da'], + }), + ('RcppZiggurat', '0.1.6', { + 'checksums': ['9c78255ca476c945c05a564d1e4da363de714d890e0e27f3b252fd73c50eed71'], + }), + ('Rfast', '2.0.7', { + 'checksums': ['8f86159a4760a7124e1c91ae0b022c7e496f81590ea4e4af702bea44e8dedf8f'], + }), + ('Rfast2', '0.1.4', { + 'checksums': ['494b777a86342aae0a6a5f0eb189337b846ef2929964672c0f010d93699d0d63'], + }), + ('MXM', version, { + 'checksums': ['943d7d3ff8496bad43329614922795b0777fa0787fdfd98f71d90a1a9c952497'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['MXM'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 72d0887ac922..1ccecc5efcd7 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1206,6 +1206,9 @@ exts_list = [ ('SpatialExperiment', '1.6.1', { 'checksums': ['31e516e14e827e4b9fe853bc136066863dd762053012631c569ec3c00c6cbab5'], }), + ('deepSNV', '1.42.1', { + 'checksums': ['f64d43645d696af7b375c66f7dccf877d099482f8470dd18c4aba8b1f30bf22d'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb new file mode 100644 index 000000000000..1b5f6973977b --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb @@ -0,0 +1,1232 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.16' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org' +description = """Bioconductor provides tools for the analysis and coprehension + of high-throughput genomic data.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [('pkgconf', '1.9.3')] + +dependencies = [ + ('R', '4.2.2'), + ('Boost', '1.81.0'), # for mzR + ('GSL', '2.7'), # for flowClust + ('HDF5', '1.14.0'), # for rhdf5 + ('arrow-R', '11.0.0.3', versionsuffix), # required by RcisTarget +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.16/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.16/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.16/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.16/data/experiment/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +# packages updated on 18th March 2023 +exts_list = [ + ('BiocGenerics', '0.44.0', { + 'checksums': ['8518e462c1ef103ab059d059d871afc444e48f56fe6b3afdb60dc1abf6c9b09d'], + }), + ('Biobase', '2.58.0', { + 'checksums': ['db798af54eb18d83242b1ffbb1fa35b5bc0256cedf86b9a6519e2d786d20e566'], + }), + ('S4Vectors', '0.36.2', { + 'checksums': ['68b441289882bde641a1d736287b2dfb837c21b21e18b127b9fee1fc5d792c8c'], + }), + ('IRanges', '2.32.0', { + 'checksums': ['097935916b5cb33804e1ea09fa6c4ee7ddeaa03eef99138a05b1896b28dc6a4b'], + }), + ('GenomeInfoDbData', '1.2.9', { + 'checksums': ['e63a719a8eceefeda39fc95de83e7aa41caad39705efc712a44ab4021adc45fa'], + }), + ('GenomeInfoDb', '1.34.9', { + 'checksums': ['2bbb094636bf628447ed4c49b4cd96c164264d012a59f0fe5982f12e6a6bc956'], + }), + ('zlibbioc', '1.44.0', { + 'checksums': ['8b2616b722e2d610cdd41aba1a94b987ab017e0bfff63f6ce66f191e81abe530'], + }), + ('XVector', '0.38.0', { + 'checksums': ['e9ba0ec3f4124c6f0ce13c4d562e7e4419f8aa5db4283092574a63a207f4ed79'], + }), + ('Biostrings', '2.66.0', { + 'checksums': ['7312c508bc2fe6ea3da75edd621b41a35929f9dbdca16d25eb3724ca2cd206fd'], + }), + ('KEGGREST', '1.38.0', { + 'checksums': ['ec9fe4b9e11858ba1236c22c9058ea3b3e6967168c847b01003b15d1afb94318'], + }), + ('AnnotationDbi', '1.60.2', { + 'checksums': ['0f52a460cefc40919273463648656c306640cf82afee3bd0fd2941dbde16eeb0'], + }), + ('GenomicRanges', '1.50.2', { + 'checksums': ['37fdc2074f17b833002c906998b09c88174c054bc5dd9fffdba1f76c4d5d668d'], + }), + ('BiocParallel', '1.32.5', { + 'checksums': ['395ed5c19fb706ca73c841c843c3a89f8a88f774a26415bfdbac0dca92a5a6f9'], + }), + ('Rhtslib', '2.0.0', { + 'checksums': ['5098bf9f4e8bbbe7eea3d63480c5c970af87b68998d625a2ec0f12b2393727e6'], + }), + ('Rsamtools', '2.14.0', { + 'checksums': ['5fe4f80752459f6f1691320ffeffd2d7d17d52dcef60c7a7035fd714ac86a471'], + }), + ('MatrixGenerics', '1.10.0', { + 'checksums': ['09fbea178608186571acabc18cd2b81fe5c7aa2d143f5d456ceaed55e01b4815'], + }), + ('DelayedArray', '0.24.0', { + 'checksums': ['d764b4f487b49ca04150ea7d8f5f180683cd80575d67a162e4a99cd52bd8815a'], + }), + ('SummarizedExperiment', '1.28.0', { + 'checksums': ['96e5e4f496ce32d8c812a7483d9208aa1b89cbf6c0342bd53c95c419bad92721'], + }), + ('GenomicAlignments', '1.34.1', { + 'checksums': ['1af0675483cd233ebc4c6d086ffec0c054e0066c424ccea97bc4ec825824e8b0'], + }), + ('ShortRead', '1.56.1', { + 'checksums': ['6baea2227937d6458d25dc590ae4d7209efe071fce8d3859e4c97266989476b7'], + }), + ('graph', '1.76.0', { + 'checksums': ['8c0ddb6d131a88d585bcf3c1e922465fbc40d6d40ba718c8a869f5f9b6ecabc1'], + }), + ('affyio', '1.68.0', { + 'checksums': ['2b3a5fc98ed39b6113031ea989f9cc9271077224cce7d6c83d1a4ef275faacad'], + }), + ('preprocessCore', '1.60.2', { + 'installopts': 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}), + ('SamSPECTRAL', '1.52.0', { + 'checksums': ['b8f85ce42b62b42c6fe6fd7fac7501e4329a359ad9126190207da9607c88f0ea'], + }), + ('ddPCRclust', '1.18.0', { + 'checksums': ['c27706a922d11d49a0a4f269df9de6882d81140eecf8a726220cd52b6db8372c'], + }), + ('feature', '1.2.15', { + 'checksums': ['de38292b7e800068a20824e2a9e7d5d4d0b465b7925db0d165346aa5030ff67b'], + }), + ('flowMerge', '2.46.0', { + 'checksums': ['3634723fd87b1bae71e2cd9e646e98cecc891521b4f2e9ff3ff388362b8b21eb'], + }), + ('SpatialExperiment', '1.8.1', { + 'checksums': ['0fdfc5642dde227b73d81812b6641f2d10223de66892b9d61ac80664cd6cbacd'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.1.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.1.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 000000000000..367d0c8c5f7a --- /dev/null +++ b/easybuild/easyconfigs/r/R-tesseract/R-tesseract-5.1.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,58 @@ +easyblock = 'Bundle' + +name = 'R-tesseract' +version = '5.1.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/package=tesseract' +description = "The R extension for using tesseract" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [('pkgconf', '1.8.0')] + +dependencies = [ + ('R', '4.2.1'), + ('poppler', '22.12.0'), + ('tesseract', '5.3.0'), +] + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('askpass', '1.1', { + 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], + }), + ('qpdf', '1.3.2', { + 'checksums': ['d9c905a4879274d72de0c638f2e14737ec0a59895cbba9814e05c62b43e8e976'], + }), + ('pdftools', '3.3.3', { + 'checksums': ['ffc0dfa5205ac3c26ee22713289784cb6b9aada6c21417d79bfd4d7f5bd5909c'], + }), + ('rappdirs', '0.3.3', { + 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], + }), + ('tesseract', version, { + 'preinstallopts': 'INCLUDE_DIR="$EBROOTTESSERACT/include/tesseract -I$EBROOTLEPTONICA/include/leptonica"' + + ' LIB_DIR=$EBROOTTESSERACT/lib', + 'checksums': ['6dae7cbc1d4cf6decabb2d1c56d95b5eb6a0a4a1cbc9f9a1c274ba558b31cdfa'], + }), +] + +sanity_check_paths = { + 'files': ['tesseract/libs/tesseract.%s' % SHLIB_EXT, 'tesseract/R/tesseract'], + 'dirs': ['askpass', 'qpdf', 'pdftools', 'rappdirs'], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb b/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb new file mode 100644 index 000000000000..fbc8b3c32f94 --- /dev/null +++ b/easybuild/easyconfigs/r/R-transport/R-transport-0.13-0-foss-2021b.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'R-transport' +local_rpkg = 'transport' +version = '0.13-0' + +homepage = 'https://cran.r-project.org/package=transport' +description = "transport: Computation of Optimal Transport Plans and Wasserstein Distances" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/transport/', + 'https://cran.r-project.org/src/contrib/', +] +sources = ['%s_%%(version)s.tar.gz' % local_rpkg] +checksums = ['c55efbdd93e36e92ef39e4b9529ee64c3c7ecb965d77ec9c469a7c56c93f5f57'] + +dependencies = [ + ('R', '4.1.2'), +] + +options = {'modulename': local_rpkg} + +sanity_check_paths = { + 'files': ['transport/R/transport', 'transport/libs/transport.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index 6175f90d8341..7f0e053f59b0 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -3360,6 +3360,15 @@ exts_list = [ ('geeM', '0.10.1', { 'checksums': ['fe76a32981b55835095041e777d1cf2e9ce43edb8d9488db56279f7cb6f43fe5'], }), + ('PMA', '1.2.1', { + 'checksums': ['3a155b89e380273dfd4ab301c422184a3f6d4679dc9e3d1bb65939392af511e6'], + }), + ('unikn', '0.8.0', { + 'checksums': ['77954418cf5475e57ccd5d28edefd97f82c49cd8e148b55b1b74f55b8c1c620f'], + }), + ('ppcor', '1.1', { + 'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 76fed434942b..313583b74abb 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -1798,8 +1798,8 @@ exts_list = [ ('HWxtest', '1.1.9', { 'patches': ['HWxtest-1.1.9_add-fcommon.patch'], 'checksums': [ - 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6', # HWxtest_1.1.9.tar.gz - '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451', # HWxtest-1.1.9_add-fcommon.patch + {'HWxtest_1.1.9.tar.gz': 'a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6'}, + {'HWxtest-1.1.9_add-fcommon.patch': '4ce08c35035dbcc4edf092cdb405ae32c21c05b3786c15c0aa4bfe13bd81f451'}, ], }), ('diveRsity', '1.9.90', { @@ -2322,9 +2322,9 @@ exts_list = [ # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ - '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz - # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch - '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', + {'liquidSVM_1.2.4.tar.gz': '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'}, + {'liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch': + '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8'}, ], }), ('oddsratio', '2.0.1', { @@ -3466,6 +3466,66 @@ exts_list = [ ('varhandle', '2.0.5', { 'checksums': ['9b0ee653e0343e292547d2a7052e60a2e7d97d1d5528246862522e67346882d0'], }), + ('dlm', '1.1-6', { + 'checksums': ['89dd4130ea3a5213244c66b313fed0a74cdcc96d3e70285b14cf3fe5f354ae57'], + }), + ('PMA', '1.2.1', { + 'checksums': ['3a155b89e380273dfd4ab301c422184a3f6d4679dc9e3d1bb65939392af511e6'], + }), + ('unikn', '0.8.0', { + 'checksums': ['77954418cf5475e57ccd5d28edefd97f82c49cd8e148b55b1b74f55b8c1c620f'], + }), + ('ppcor', '1.1', { + 'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'], + }), + ('tvem', '1.3.1', { + 'checksums': ['931085e210891744df64288ce174dface7a68bdb6b21a5883a9d83bb66a132c3'], + }), + ('berryFunctions', '1.22.0', { + 'checksums': ['8d8578d746e8e4f7a1deb0b1d49ff8603c5e51504d5fe549bcba54f20fe9d498'], + }), + ('cld2', '1.2.4', { + 'checksums': ['79e04de836812a980406a540c0f022926ba71c2bf5294ad5eaa437a9c33e615b'], + }), + ('crfsuite', '0.4.1', { + 'checksums': ['be4f8e7773caa2e3ceac7e35d47ef323f6b121d2b2da1e3b90b4e3b4fc7da46e'], + }), + ('doc2vec', '0.2.0', { + 'checksums': ['db3853685072554402434ea699d703e01ac7818044cf47a2ee7d0e1040858908'], + }), + ('fastDummies', '1.6.3', { + 'checksums': ['bd3934fe19d7dff2723438bbb7b89334118143f8ce151d98477ae964ee5d81df'], + }), + ('quanteda', '3.2.3', { + 'checksums': ['f34b0e89ad7795eed0d624fb57a9fb924175a03df0c23fc1f71eefe6a14d93ae'], + }), + ('rlist', '0.4.6.2', { + 'checksums': ['ebde658d897c8a27a90ebb892b9e2bad15e2ad75557a7352fb08cbb5604e0997'], + }), + ('ISOweek', '0.6-2', { + 'checksums': ['b58a37b61ee772ea2704d510e9fce69dea4dd641b45124d566242825df4530b8'], + }), + ('sentometrics', '1.0.0', { + 'checksums': ['b5c238bb72f36331cb1ed63b581a9a2a73cefc96f80bf770b0e064a89fe31b1b'], + }), + ('tau', '0.0-24', { + 'checksums': ['f08d9fc92ed11ec01f7da12ccf98862e36ef8bb69d5e42584a08b46cea6917e1'], + }), + ('textcat', '1.0-8', { + 'checksums': ['cb650147576bae9c78381524831c9fcc85c76177274672098aac1860aa39749e'], + }), + ('textplot', '0.2.2', { + 'checksums': ['6e99a204b4be2ccd317978eda900b923e0e0a0f34217405777a0eb5fcc80e2a9'], + }), + ('udpipe', '0.8.11', { + 'checksums': ['522900de24d1f0f4f15e6b26df5521ac6efaf63c5fcfc35171a78275b3633233'], + }), + ('word2vec', '0.3.4', { + 'checksums': ['53db1d8c8d6af8ace8636adec1e254b0b61fbdba77ba7a295afc7da3eb4e4362'], + }), + ('epitools', '0.5-10.1', { + 'checksums': ['b418854de1fcedd126f3bf19dc27e8a71ee6efae5371098ab64a53a2d51d164b'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index dd02af827b61..e8a09bc8b642 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -3537,6 +3537,60 @@ exts_list = [ ('varhandle', '2.0.5', { 'checksums': ['9b0ee653e0343e292547d2a7052e60a2e7d97d1d5528246862522e67346882d0'], }), + ('dlm', '1.1-6', { + 'checksums': ['89dd4130ea3a5213244c66b313fed0a74cdcc96d3e70285b14cf3fe5f354ae57'], + }), + ('PMA', '1.2.1', { + 'checksums': ['3a155b89e380273dfd4ab301c422184a3f6d4679dc9e3d1bb65939392af511e6'], + }), + ('unikn', '0.8.0', { + 'checksums': ['77954418cf5475e57ccd5d28edefd97f82c49cd8e148b55b1b74f55b8c1c620f'], + }), + ('ppcor', '1.1', { + 'checksums': ['6a78f0c4d9caa17ab0252c5d351c2371e4ffb9047ebd13964877018dd6142bf5'], + }), + ('berryFunctions', '1.22.0', { + 'checksums': ['8d8578d746e8e4f7a1deb0b1d49ff8603c5e51504d5fe549bcba54f20fe9d498'], + }), + ('cld2', '1.2.4', { + 'checksums': ['79e04de836812a980406a540c0f022926ba71c2bf5294ad5eaa437a9c33e615b'], + }), + ('crfsuite', '0.4.1', { + 'checksums': ['be4f8e7773caa2e3ceac7e35d47ef323f6b121d2b2da1e3b90b4e3b4fc7da46e'], + }), + ('doc2vec', '0.2.0', { + 'checksums': ['db3853685072554402434ea699d703e01ac7818044cf47a2ee7d0e1040858908'], + }), + ('fastDummies', '1.6.3', { + 'checksums': ['bd3934fe19d7dff2723438bbb7b89334118143f8ce151d98477ae964ee5d81df'], + }), + ('quanteda', '3.3.0', { + 'checksums': ['03256faf63455d16d643349a34b068d0bf69506a0e952b99ab2391e6423663a5'], + }), + ('rlist', '0.4.6.2', { + 'checksums': ['ebde658d897c8a27a90ebb892b9e2bad15e2ad75557a7352fb08cbb5604e0997'], + }), + ('ISOweek', '0.6-2', { + 'checksums': ['b58a37b61ee772ea2704d510e9fce69dea4dd641b45124d566242825df4530b8'], + }), + ('sentometrics', '1.0.0', { + 'checksums': ['b5c238bb72f36331cb1ed63b581a9a2a73cefc96f80bf770b0e064a89fe31b1b'], + }), + ('tau', '0.0-24', { + 'checksums': ['f08d9fc92ed11ec01f7da12ccf98862e36ef8bb69d5e42584a08b46cea6917e1'], + }), + ('textcat', '1.0-8', { + 'checksums': ['cb650147576bae9c78381524831c9fcc85c76177274672098aac1860aa39749e'], + }), + ('textplot', '0.2.2', { + 'checksums': ['6e99a204b4be2ccd317978eda900b923e0e0a0f34217405777a0eb5fcc80e2a9'], + }), + ('udpipe', '0.8.11', { + 'checksums': ['522900de24d1f0f4f15e6b26df5521ac6efaf63c5fcfc35171a78275b3633233'], + }), + ('word2vec', '0.3.4', { + 'checksums': ['53db1d8c8d6af8ace8636adec1e254b0b61fbdba77ba7a295afc7da3eb4e4362'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/RE2/RE2-2023-03-01-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/RE2/RE2-2023-03-01-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..b43aca007514 --- /dev/null +++ b/easybuild/easyconfigs/r/RE2/RE2-2023-03-01-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = "CMakeMake" + +name = 'RE2' +version = '2023-03-01' + +homepage = 'https://github.com/google/re2' +description = """ +RE2 is a fast, safe, thread-friendly alternative to backtracking regular +expression engines like those used in PCRE, Perl, and Python. It is a C++ +library. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +github_account = 'google' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['7a9a4824958586980926a300b4717202485c4b4115ac031822e29aa4ef207e48'] + +builddependencies = { + ('binutils', '2.39'), + ('CMake', '3.24.3'), +} + +sanity_check_paths = { + 'files': ['lib/libre2.a'], + 'dirs': ['include/re2'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb new file mode 100644 index 000000000000..4acf0146bc4f --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-6.26.10-foss-2022b.eb @@ -0,0 +1,55 @@ +name = 'ROOT' +version = '6.26.10' + +homepage = 'https://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = ['https://root.cern.ch/download/'] +sources = ['%(namelower)s_v%(version)s.source.tar.gz'] +checksums = ['8e56bec397104017aa54f9eb554de7a1a134474fe0b3bb0f43a70fc4fabd625f'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('GSL', '2.7'), + ('libxml2', '2.10.3'), + ('PCRE', '8.45'), + ('CFITSIO', '4.2.0'), + ('freetype', '2.12.1'), + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('zlib', '1.2.12'), + ('X11', '20221110'), + ('Mesa', '22.2.4'), + ('libGLU', '9.0.2'), + ('GL2PS', '1.4.2'), + ('FFTW', '3.3.10'), + ('SQLite', '3.39.4'), + ('XZ', '5.2.7'), + ('libpng', '1.6.38'), +] + +# NOTE: Ensure that each configopts string begins with a blank +# disable some components +configopts = " -Dxrootd=OFF -Dmysql=OFF -Dkrb5=OFF -Dodbc=OFF -Doracle=OFF -Dpgsql=OFF -Dqt=OFF" + +# make sure some components are enabled +configopts += " -Dpcre=ON -Dzlib=ON -Dpyroot=ON" +configopts += " -Dunuran=ON -Dexplicitlink=ON -Dminuit2=ON -Droofit=ON " + +# Add component-specific settings based on dependencies +configopts += ' -Dfftw3=ON -Dgsl=ON -DOpenGL_GL_PREFERENCE=GLVND' + +# Set C++ standard to C++17 for better stability +configopts += ' -DCMAKE_CXX_STANDARD=17' + +configopts += " -Dgallium-drivers=swrast" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/RPostgreSQL/RPostgreSQL-0.7-5-foss-2022a.eb b/easybuild/easyconfigs/r/RPostgreSQL/RPostgreSQL-0.7-5-foss-2022a.eb new file mode 100644 index 000000000000..88f4b40198be --- /dev/null +++ b/easybuild/easyconfigs/r/RPostgreSQL/RPostgreSQL-0.7-5-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'Bundle' + +name = 'RPostgreSQL' +version = '0.7-5' + +homepage = 'https://cran.r-project.org/package=tesseract' +description = """ +Database interface and 'PostgreSQL' driver for 'R'. This package provides a +Database Interface 'DBI' compliant driver for 'R' to access 'PostgreSQL' +database systems.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('R', '4.2.1'), + ('PostgreSQL', '14.4'), +] + +exts_defaultclass = 'RPackage' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + (name, version, { + 'checksums': ['6b5401ee55bd948ae7bc84520d789ceb422533a7d5e5bd6e10e3b54447f29fa1'], + }), +] + +sanity_check_paths = { + 'files': ['RPostgreSQL/libs/RPostgreSQL.%s' % SHLIB_EXT, 'RPostgreSQL/R/RPostgreSQL'], + 'dirs': [], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..9594b13fd9d8 --- /dev/null +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'RapidJSON' +version = '1.1.0' + +homepage = 'https://rapidjson.org' +description = "A fast JSON parser/generator for C++ with both SAX/DOM style API" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/Tencent/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-compiler-errors.patch'] +checksums = [ + 'bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e', # v1.1.0.tar.gz + # %(name)s-%(version_major_minor)s.0_fix-compiler-errors.patch + '2e40ef6c46bf355feac16cd84faad5b7aca0ad54273117b85534b1b781f411c7', +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['lib/pkgconfig/%(name)s.pc'], + 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb new file mode 100644 index 000000000000..0e32ebaa9e02 --- /dev/null +++ b/easybuild/easyconfigs/r/Raven/Raven-1.8.1-GCC-11.2.0.eb @@ -0,0 +1,63 @@ +easyblock = "CMakeNinja" + +name = "Raven" +version = "1.8.1" + +homepage = "https://github.com/lbcb-sci/raven" +description = "Raven is a de novo genome assembler for long uncorrected reads." + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ["https://github.com/lbcb-sci/raven/archive/refs/tags/"] +sources = ["%(version)s.tar.gz"] +checksums = ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Ninja', '1.10.2'), +] + +preinstallopts = "export CMAKE_BUILD_PARALLEL_LEVEL=%(parallel)s && " +configopts = '-DRAVEN_BUILD_EXE=1 -G Ninja ' +configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' + +dependencies = [ + ('Python', '3.9.6'), + ('zlib', '1.2.11'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} + +# inject addition CMake options to make sure that Python dependency is actually used +local_ravenpy_preinstallopts = r"""sed -i 's|cmake_args += \["-GNinja"\]|cmake_args += \[""" +local_ravenpy_preinstallopts += r'"-GNinja", "-DPYBIND11_FINDPYTHON=ON", "-DPython_FIND_STRATEGY=LOCATION",' +local_ravenpy_preinstallopts += r""" "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python"\]|' setup.py && """ + +exts_list = [ + (name, version, { + 'modulename': 'ravenpy', + 'source_urls': ['https://github.com/lbcb-sci/raven/archive/refs/tags/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['00009e9027761fa28313db4e2b5c5f40ebc10e6631b43b755e321ac6bbcc2c06'], + 'preinstallopts': local_ravenpy_preinstallopts, + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/raven'], + 'dirs': [], +} + +sanity_check_commands = [ + "export PYTHONNOUSERSITE=1 && python%(pyshortver)s -m pip check", + "raven --help" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb new file mode 100644 index 000000000000..dc290fcc04d4 --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-4.2.0.eb @@ -0,0 +1,63 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '4.2.0' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + }), + ('reframe', version, { + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['f1d38133023b37d01fdee46b2bf472f8fd36bf410d1c909db043b9f9d7df6122'], + }), +] + +postinstallcmds = [ + "cp -a hpctestlib tools tutorials %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'hpctestlib', 'lib', 'tools', 'tutorials'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +modextrapaths = { + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/ReaxFF/ReaxFF-2.0-GCC-11.3.0.eb b/easybuild/easyconfigs/r/ReaxFF/ReaxFF-2.0-GCC-11.3.0.eb new file mode 100644 index 000000000000..a3082257b1f2 --- /dev/null +++ b/easybuild/easyconfigs/r/ReaxFF/ReaxFF-2.0-GCC-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'ReaxFF' +version = '2.0' + +homepage = 'https://www.engr.psu.edu/adri/ReaxffManual.aspx' + +description = """ +REAXFF Reactive force field program +""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a62829d25b6eb5c311206a89a892e1de6fd3ee33cae40489901bb9f50d53f4d2'] + +download_instructions = """ +Register at https://www.engr.psu.edu/adri/Home.aspx and follow instructions +""" + +buildopts = 'SUFFIX="-c -O3 -std=legacy"' + +files_to_copy = [ + (['reac'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/reac'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.5-foss-2022a.eb b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.5-foss-2022a.eb new file mode 100644 index 000000000000..d7e8df4c81de --- /dev/null +++ b/easybuild/easyconfigs/r/RepeatMasker/RepeatMasker-4.1.5-foss-2022a.eb @@ -0,0 +1,57 @@ +easyblock = 'Tarball' + +name = 'RepeatMasker' +version = '4.1.5' + +homepage = 'https://www.repeatmasker.org/' +description = """RepeatMasker is a program that screens DNA sequences for interspersed repeats + and low complexity DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://www.repeatmasker.org/%(name)s'] +sources = [ + SOURCE_TAR_GZ, + # optional but recommended: RepBase RepeatMasker Edition + # requires subscription and academic license, download from here: https://www.girinst.org/server/RepBase/index.php + # { + # 'filename': 'RepBaseRepeatMaskerEdition-20181026.tar.gz', + # 'extract_cmd': "tar -xzf %s -C %(builddir)s/%(name)s/Libraries --strip-components 1", + # }, +] +checksums = ['16e07f9efd99adf15f4492b0e334df5ad4ea6ca38ddf62bdd180d257f2f4753f'] + +dependencies = [ + ('Python', '3.10.4'), + ('Perl', '5.34.1'), + ('TRF', '4.09.1'), + ('h5py', '3.7.0'), + # At least one search engine of: RMBlast, HMMER, ABBlast/WUBlast, Cross_Match + ('HMMER', '3.3.2'), + ('RMBlast', '2.13.0'), +] + +local_default_search_engine = 'RMBlast' + +local_config_command = 'cd %(installdir)s &&' +local_config_command += './configure -perlbin "$EBROOTPERL/bin/perl" -trf_prgm "$EBROOTTRF/bin/trf" ' +local_config_command += '-hmmer_dir "$EBROOTHMMER/bin" -rmblast_dir "$EBROOTRMBLAST/bin" ' +local_config_command += '-default_search_engine %s' % local_default_search_engine.lower() + +postinstallcmds = [local_config_command] + +fix_perl_shebang_for = ['RepeatMasker'] + +sanity_check_paths = { + 'files': ['RepeatMasker', 'RepeatMaskerConfig.pm'], + 'dirs': ['Libraries', 'util'], +} + +sanity_check_commands = ['RepeatMasker -help'] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': '', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RevBayes/RevBayes-1.2.1-gompi-2022a.eb b/easybuild/easyconfigs/r/RevBayes/RevBayes-1.2.1-gompi-2022a.eb new file mode 100644 index 000000000000..525ec2e7c03f --- /dev/null +++ b/easybuild/easyconfigs/r/RevBayes/RevBayes-1.2.1-gompi-2022a.eb @@ -0,0 +1,40 @@ +# easybuild easyconfig +# +# John Dey +# Fred Hutchinson Cancer Research Center - Seattle Washington - US +easyblock = 'CmdCp' + +name = 'RevBayes' +version = '1.2.1' + +homepage = 'https://revbayes.github.io' +description = """RevBayes provides an interactive environment for statistical computation in + phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in + evolutionary biology, particularly phylogenetics.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/revbayes/revbayes/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['58c320ee7251a7a244aba57b471a6e695f3db8196ea4c9381bb2bc1076bcedfa'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Boost', '1.79.0'), +] + +start_dir = 'projects/cmake' +local_cmd = './build.sh -mpi true -DCMAKE_CXX_FLAGS="-pthread" -DBoost_NO_BOOST_CMAKE=ON' +cmds_map = [('', local_cmd)] + +files_to_copy = [(['projects/cmake/rb-mpi'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/rb-mpi'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Rtree/Rtree-1.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Rtree/Rtree-1.0.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..5650717ef683 --- /dev/null +++ b/easybuild/easyconfigs/r/Rtree/Rtree-1.0.1-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Rtree' +version = '1.0.1' + +homepage = 'https://toblerity.org/rtree/' +description = """Rtree is a ctypes Python wrapper of libspatialindex that provides a number of advanced spatial + indexing features for the spatially curious Python user.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['222121699c303a64065d849bf7038b1ecabc37b65c7fa340bedb38ef0e805429'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('libspatialindex', '1.9.3'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a.eb b/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a.eb new file mode 100644 index 000000000000..9f53672f0cb2 --- /dev/null +++ b/easybuild/easyconfigs/r/rgdal/rgdal-1.6-6-foss-2022a.eb @@ -0,0 +1,31 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'RPackage' + +name = 'rgdal' +version = '1.6-6' + +homepage = 'https://rgdal.r-forge.r-project.org/' +description = """Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and + access to projection/transformation operations from the 'PROJ.4' library.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['d742d7aadfc004771e61cac28a1faffeb4dbda981dea19115be11c541087399a'] + +dependencies = [ + ('R', '4.2.1'), + ('GDAL', '3.5.0'), +] + +sanity_check_paths = { + 'files': ['%(name)s/R/%(name)s'], + 'dirs': [], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/rioxarray/rioxarray-0.14.0-foss-2022a.eb b/easybuild/easyconfigs/r/rioxarray/rioxarray-0.14.0-foss-2022a.eb new file mode 100644 index 000000000000..57c9a4816f34 --- /dev/null +++ b/easybuild/easyconfigs/r/rioxarray/rioxarray-0.14.0-foss-2022a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'rioxarray' +version = '0.14.0' + +homepage = 'https://github.com/corteva/rioxarray' +description = "geospatial xarray extension powered by rasterio" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('rasterio', '1.3.4'), + ('pyproj', '3.4.0'), + ('xarray', '2022.6.0'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['bbbda47fd7eb04c0986df553f11aa0bdbc9846e75601b8ebd704fc8573bfb835'] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/ripunzip/ripunzip-0.4.0.eb b/easybuild/easyconfigs/r/ripunzip/ripunzip-0.4.0.eb new file mode 100644 index 000000000000..ef9b2d15dd99 --- /dev/null +++ b/easybuild/easyconfigs/r/ripunzip/ripunzip-0.4.0.eb @@ -0,0 +1,484 @@ +easyblock = 'Cargo' + +name = 'ripunzip' +version = '0.4.0' + +homepage = 'https://github.com/google/ripunzip' +description = "A tool to unzip files in parallel." + +toolchain = SYSTEM + +crates = [ + ('adler', '1.0.2'), + ('aes', '0.7.5'), + ('aho-corasick', '0.7.20'), + ('anyhow', '1.0.66'), + ('arbitrary', '1.2.0'), + ('arrayvec', '0.5.2'), + ('atty', '0.2.14'), + ('autocfg', '1.1.0'), + ('base64', '0.13.1'), + ('base64ct', '1.5.3'), + ('bitflags', '1.3.2'), + ('block-buffer', '0.10.3'), + ('bstr', '0.2.17'), + ('bumpalo', '3.11.1'), + ('byteorder', '1.4.3'), + ('bytes', '1.3.0'), + ('bzip2', '0.4.3'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cast', '0.3.0'), + ('cc', '1.0.77'), + ('cfg-if', '1.0.0'), + ('cipher', '0.3.0'), + ('clap', '2.34.0'), + ('clap', '4.0.29'), + ('clap_derive', '4.0.21'), + ('clap_lex', '0.3.0'), + ('console', '0.15.2'), + ('constant_time_eq', '0.1.5'), + ('core-foundation', '0.9.3'), + ('core-foundation-sys', '0.8.3'), + ('cpufeatures', '0.2.5'), + ('crc32fast', '1.3.2'), + ('criterion', '0.3.6'), + ('criterion-plot', '0.4.5'), + ('crossbeam-channel', '0.5.6'), + ('crossbeam-deque', '0.8.2'), + ('crossbeam-epoch', '0.9.13'), + ('crossbeam-utils', '0.8.14'), + ('crypto-common', '0.1.6'), + ('csv', '1.1.6'), + ('csv-core', '0.1.10'), + ('derive_arbitrary', '1.2.1'), + ('digest', '0.10.6'), + ('either', '1.8.0'), + ('encode_unicode', '0.3.6'), + ('encoding_rs', '0.8.31'), + ('env_logger', '0.10.0'), + ('errno', '0.2.8'), + ('errno-dragonfly', '0.1.2'), + ('fastrand', '1.8.0'), + ('flate2', '1.0.25'), + ('fnv', '1.0.7'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('form_urlencoded', '1.1.0'), + ('futures', '0.3.25'), + ('futures-channel', '0.3.25'), + 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Library, or ROCm SMI +library, is part of the Radeon Open Compute ROCm software stack. It is a C +library for Linux that provides a user space interface for applications to +monitor and control GPU applications.""" +docurls = ['https://rocmdocs.amd.com'] + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ["https://github.com/RadeonOpenCompute/rocm_smi_lib/archive/"] +sources = ["rocm-%(version)s.tar.gz"] +checksums = ['27a6d851a493a3ab11ca3af079b4a0509579aa7bab2b2891af3bdf816a456ff0'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['bin/rocm-smi'], + 'dirs': [], +} + +sanity_check_commands = ['rocm-smi --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..e74ae172df4a --- /dev/null +++ b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-12.2.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'ruamel.yaml' +version = '0.17.21' + +homepage = 'https://sourceforge.net/projects/ruamel-yaml' +description = "ruamel.yaml is a YAML 1.2 loader/dumper package for Python." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True + +exts_list = [ + ('ruamel.yaml.clib', '0.2.7', { + 'modulename': False, + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + }), + (name, version, { + 'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'], + }), + ('configobj', '5.0.8', { + 'checksums': ['6f704434a07dc4f4dc7c9a745172c1cad449feb548febd9f7fe362629c627a97'], + }), + ('lz4', '4.3.2', { + 'checksums': ['e1431d84a9cfb23e6773e72078ce8e65cad6745816d4cbf9ae67da5ea419acda'], + }), + ('ruamel.yaml.base', '0.3.2', { + 'checksums': ['88b6edc8ace60c12d98f05fda22e5d9d69ba9a4b531cf54783142151145b0372'], + }), + ('ruamel.yaml.convert', '0.3.2', { + 'checksums': ['065ed9492a3189291d5bc0256709afc0231b52e4a01376fc91cf1757560ac9c4'], + }), + ('ruamel.yaml.cmd', '0.6.3', { + 'checksums': ['f4ebce7d6d9d53afae84d7efd79f8d6c3dcad56e0e6be3a5d2370be0e04acea0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/yaml'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["yaml --help"] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..0354e336f08b --- /dev/null +++ b/easybuild/easyconfigs/r/ruffus/ruffus-2.8.4-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'ruffus' +version = '2.8.4' + +homepage = 'http://www.ruffus.org.uk/' +description = """Ruffus is a Computation Pipeline library for python. It is open-sourced, powerful and user-friendly, + and widely used in science and bioinformatics.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['6cd3d96e459a1aedcc10341f14fddedfdc13664551757fcd429a241de63826aa'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('Graphviz', '5.0.0'), +] + +download_dep_fail = True + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import ruffus.graph'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2022a.eb b/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2022a.eb new file mode 100644 index 000000000000..73bcca7c937e --- /dev/null +++ b/easybuild/easyconfigs/r/rustworkx/rustworkx-0.12.1-foss-2022a.eb @@ -0,0 +1,169 @@ +easyblock = "CargoPythonPackage" + +name = 'rustworkx' +version = '0.12.1' + +homepage = 'https://github.com/Qiskit/rustworkx' +description = """rustworkx (previously retworkx) is a general purpose graph library for Python written in Rust to take +advantage of the performance and safety that Rust provides. It is designed to provide a high performance general +purpose graph library for any Python application.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Rust', '1.65.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +crates = [ + ('ahash', '0.7.6'), + ('autocfg', '1.1.0'), + ('bitflags', '1.3.2'), + ('cfg-if', '1.0.0'), + ('crossbeam-channel', '0.5.4'), + ('crossbeam-deque', '0.8.1'), + ('crossbeam-epoch', '0.9.8'), + ('crossbeam-utils', '0.8.8'), + ('either', '1.6.1'), + ('fixedbitset', '0.4.2'), + ('getrandom', '0.2.6'), + ('hashbrown', '0.11.2'), + ('hermit-abi', '0.1.19'), + ('indexmap', '1.7.0'), + ('indoc', '1.0.6'), + ('instant', '0.1.12'), + ('itoa', '1.0.2'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.126'), + ('lock_api', '0.4.7'), + ('matrixmultiply', '0.2.4'), + ('memchr', '2.5.0'), + ('memoffset', '0.6.5'), + ('ndarray', '0.13.1'), + ('num-bigint', '0.4.3'), + ('num-complex', '0.2.4'), + 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'81fa1584d3d1bcacd84c277a0dfe21f5b0f6accf4a23d04d4c6d61f1af522b4c'}, + {'serde_json-1.0.89.tar.gz': '020ff22c755c2ed3f8cf162dbb41a7268d934702f3ed3631656ea597e08fc3db'}, + {'smallvec-1.8.0.tar.gz': 'f2dd574626839106c320a323308629dcb1acfc96e32a8cba364ddc61ac23ee83'}, + {'syn-1.0.96.tar.gz': '0748dd251e24453cb8717f0354206b91557e4ec8703673a4b30208f2abaf1ebf'}, + {'target-lexicon-0.12.4.tar.gz': 'c02424087780c9b71cc96799eaeddff35af2bc513278cda5c99fc1f5d026d3c1'}, + {'unicode-ident-1.0.0.tar.gz': 'd22af068fba1eb5edcb4aea19d382b2a3deb4c8f9d475c589b6ada9e0fd493ee'}, + {'unindent-0.1.9.tar.gz': '52fee519a3e570f7df377a06a1a7775cdbfb7aa460be7e08de2b1f0e69973a44'}, + {'version_check-0.9.4.tar.gz': '49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f'}, + {'wasi-0.10.2+wasi-snapshot-preview1.tar.gz': 'fd6fbd9a79829dd1ad0cc20627bf1ed606756a7f77edff7b66b7064f9cb327c6'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SCIP/SCIP-3.2.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SCIP/SCIP-3.2.1-GCC-11.3.0.eb new file mode 100644 index 000000000000..ac0cfca19e8d --- /dev/null +++ b/easybuild/easyconfigs/s/SCIP/SCIP-3.2.1-GCC-11.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'SCIP' +version = '3.2.1' + +homepage = 'https://www.scipopt.org/' +description = """SCIP is currently one of the fastest non-commercial solvers for mixed integer +programming (MIP) and mixed integer nonlinear programming (MINLP). It is also a +framework for constraint integer programming and branch-cut-and-price. It +allows for total control of the solution process and the access of detailed +information down to the guts of the solver.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'scipopt' +source_urls = [GITHUB_SOURCE] +sources = ['v%s.tar.gz' % version.replace('.', '')] +checksums = ['015bdda4e681782fd03b61421b93aa3c1b913e5eea18bb8730d5fb9e4d67b4cb'] + +dependencies = [ + ('SoPlex', '2.2.1'), + ('ZIMPL', '3.3.4'), + ('GMP', '6.2.1'), + ('libreadline', '8.1'), + ('zlib', '1.2.12'), +] + +skipsteps = ['configure'] + +# prepare symlinks to installation files of dependencies +prebuildopts = 'mkdir -p lib && ' +prebuildopts += 'ln -sf "$EBROOTSOPLEX/include" "lib/spxinc" && ' +prebuildopts += 'ln -sf "$EBROOTZIMPL/include" "lib/zimplinc" && ' +prebuildopts += 'for lib in "$EBROOTSOPLEX/lib/libsoplex*.a"; do ln -sf "$lib" "lib/"; done && ' +prebuildopts += 'for lib in "$EBROOTZIMPL/lib/libzimpl*.a"; do ln -sf "$lib" "lib/"; done && ' + +# use SoPlex v2 as LP solver +buildopts = 'LPS=spx2 ' +buildopts += 'MAKESOFTLINKS=false COMP=gnu OPT=opt ' + +installopts = 'INSTALLDIR="%(installdir)s" ' +installopts += buildopts + +postinstallcmds = [ + # add extra headers to installation directory + 'cp "src/scip/misc.h" "%(installdir)s/include/scip/"', + # copy examples folder + 'cp -r "examples" "%(installdir)s/"', +] + +sanity_check_paths = { + 'files': ['bin/scip', 'lib/liblpispx2.a', 'lib/libnlpi.cppad.a', 'lib/libobjscip.a', 'lib/libscip.a'], + 'dirs': ['examples', 'include'], +} + +sanity_check_commands = ["scip -h"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SHAP/SHAP-0.41.0-foss-2022a.eb b/easybuild/easyconfigs/s/SHAP/SHAP-0.41.0-foss-2022a.eb new file mode 100644 index 000000000000..0e5be094112a --- /dev/null +++ b/easybuild/easyconfigs/s/SHAP/SHAP-0.41.0-foss-2022a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'SHAP' +version = '0.41.0' + +homepage = "https://github.com/slundberg/shap" +description = """SHAP (SHapley Additive exPlanations) is a game theoretic approach to explain the output of any + machine learning model. It connects optimal credit allocation with local explanations using the classic Shapley + values from game theory and their related extensions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('tqdm', '4.64.0'), + ('numba', '0.56.4'), +] + +# Python 3.10.4 uses poetry 1.1.13 which needs packaging "^20.4" +preinstallopts = "sed -i 's/packaging>20.9/packaging/g' setup.py && " + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.1', { + 'checksums': ['d89684b8de9e34a2a43b3460fbca07d09d6e25ce858df4d5a44240403b6178f5'], + }), + ('slicer', '0.0.7', { + 'checksums': ['f5d5f7b45f98d155b9c0ba6554fa9770c6b26d5793a3e77a1030fb56910ebeec'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['a49ea4d65aadbc845a695fa3d7ea0bdfc8c928b8e213b0feedf5868ade4b3ca5'], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb new file mode 100644 index 000000000000..1db8a8efa481 --- /dev/null +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.18.2-intel-2021b.eb @@ -0,0 +1,21 @@ +name = 'SLEPc' +version = '3.18.2' + +homepage = 'https://www.grycap.upv.es/slepc/' +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://slepc.upv.es/download/distrib'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5bd90a755934e702ab1fdb3320b9fe75ab5fc28c93d364248ea86a372fbe6a62'] + +dependencies = [('PETSc', '3.18.4')] + +petsc_arch = 'installed-arch-linux2-c-opt' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SLiM/SLiM-4.0-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SLiM/SLiM-4.0-GCC-11.2.0.eb new file mode 100644 index 000000000000..a83b635112ef --- /dev/null +++ b/easybuild/easyconfigs/s/SLiM/SLiM-4.0-GCC-11.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'SLiM' +version = '4.0' + +homepage = 'https://messerlab.org/slim' +description = """SLiM is an evolutionary simulation framework that combines a powerful engine for population + genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/MesserLab/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use_external_zlib_gsl.patch', +] +checksums = [ + 'd53ce9fc4ac00fa1dc3fc046ac21adb461ead46c1a0c54a72537a74873abf894', # v4.0.tar.gz + '7290f24ec9e04edc696aa85e3b4186cfcffa76b3c9b08bdf379ea00eac578755', # SLiM-4.0_use_external_zlib_gsl.patch +] + +builddependencies = [ + ('CMake', '3.21.1'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('GSL', '2.7'), + ('Mesa', '21.1.7'), + ('libglvnd', '1.3.3'), + ('Qt5', '5.15.2'), +] + +configopts = '-DBUILD_SLIMGUI=ON ' + +sanity_check_paths = { + 'files': ['bin/eidos', 'bin/slim'], + 'dirs': [], +} + +sanity_check_commands = [ + "eidos -usage", + "eidos -testEidos", + "slim -usage", + "slim -testSLiM", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb new file mode 100644 index 000000000000..496b738e7b59 --- /dev/null +++ b/easybuild/easyconfigs/s/SLiM/SLiM-4.0.1-GCC-11.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'SLiM' +version = '4.0.1' + +homepage = 'https://messerlab.org/slim' +description = """SLiM is an evolutionary simulation framework that combines a powerful engine for population + genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/MesserLab/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-4.0_use_external_zlib_gsl.patch', +] +checksums = [ + {'v4.0.1.tar.gz': 'a44564023db372cd438b4e6c729a4ba59200d1217a63b3694ca7903436886cc2'}, + {'SLiM-4.0_use_external_zlib_gsl.patch': '7290f24ec9e04edc696aa85e3b4186cfcffa76b3c9b08bdf379ea00eac578755'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('GSL', '2.7'), + ('Mesa', '22.0.3'), + ('libglvnd', '1.4.0'), + ('Qt5', '5.15.5'), +] + +configopts = '-DBUILD_SLIMGUI=ON ' + +sanity_check_paths = { + 'files': ['bin/eidos', 'bin/slim'], + 'dirs': [], +} + +sanity_check_commands = [ + "eidos -usage", + "eidos -testEidos", + "slim -usage", + "slim -testSLiM", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SLiM/SLiM-4.0_use_external_zlib_gsl.patch b/easybuild/easyconfigs/s/SLiM/SLiM-4.0_use_external_zlib_gsl.patch new file mode 100644 index 000000000000..894f69dd4f36 --- /dev/null +++ b/easybuild/easyconfigs/s/SLiM/SLiM-4.0_use_external_zlib_gsl.patch @@ -0,0 +1,161 @@ +commit 2ba4892b9327e5d21fdd712e178447d2ecd3665a +Author: Ake Sandgren +Date: Wed Aug 24 08:15:39 2022 +0200 + + Use external Zlib and GSL instead of internal ones. + And use correctly names zlib functions. + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 487c7bcd..0aae03ea 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -157,18 +157,20 @@ endif() + #endif() + + # GSL +-set(TARGET_NAME gsl) +-file(GLOB_RECURSE GSL_SOURCES ${PROJECT_SOURCE_DIR}/gsl/*.c ${PROJECT_SOURCE_DIR}/gsl/*/*.c) +-set(GSL_INCLUDES ${PROJECT_SOURCE_DIR}/gsl ${PROJECT_SOURCE_DIR}/gsl/specfunc ${PROJECT_SOURCE_DIR}/gsl/blas ${PROJECT_SOURCE_DIR}/gsl/rng ${PROJECT_SOURCE_DIR}/gsl/cdf ${PROJECT_SOURCE_DIR}/gsl/vector ${PROJECT_SOURCE_DIR}/gsl/err ${PROJECT_SOURCE_DIR}/gsl/sys ${PROJECT_SOURCE_DIR}/gsl/randist ${PROJECT_SOURCE_DIR}/gsl/matrix ${PROJECT_SOURCE_DIR}/gsl/cblas ${PROJECT_SOURCE_DIR}/gsl/complex ${PROJECT_SOURCE_DIR}/gsl/block ${PROJECT_SOURCE_DIR}/gsl/linalg) +-add_library(${TARGET_NAME} STATIC ${GSL_SOURCES}) +-target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES}) ++# Use external GSL instead ++#set(TARGET_NAME gsl) ++#file(GLOB_RECURSE GSL_SOURCES ${PROJECT_SOURCE_DIR}/gsl/*.c ${PROJECT_SOURCE_DIR}/gsl/*/*.c) ++#set(GSL_INCLUDES ${PROJECT_SOURCE_DIR}/gsl ${PROJECT_SOURCE_DIR}/gsl/specfunc ${PROJECT_SOURCE_DIR}/gsl/blas ${PROJECT_SOURCE_DIR}/gsl/rng ${PROJECT_SOURCE_DIR}/gsl/cdf ${PROJECT_SOURCE_DIR}/gsl/vector ${PROJECT_SOURCE_DIR}/gsl/err ${PROJECT_SOURCE_DIR}/gsl/sys ${PROJECT_SOURCE_DIR}/gsl/randist ${PROJECT_SOURCE_DIR}/gsl/matrix ${PROJECT_SOURCE_DIR}/gsl/cblas ${PROJECT_SOURCE_DIR}/gsl/complex ${PROJECT_SOURCE_DIR}/gsl/block ${PROJECT_SOURCE_DIR}/gsl/linalg) ++#add_library(${TARGET_NAME} STATIC ${GSL_SOURCES}) ++#target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES}) + + # ZLIB +-set(TARGET_NAME eidos_zlib) +-file(GLOB_RECURSE ZLIB_SOURCES ${PROJECT_SOURCE_DIR}/eidos_zlib/*.c) +-set(ZLIB_INCLUDES ${PROJECT_SOURCE_DIR}/eidos_zlib) +-add_library(${TARGET_NAME} STATIC ${ZLIB_SOURCES}) +-target_include_directories(${TARGET_NAME} PUBLIC) ++# Use external Zlib instead ++#set(TARGET_NAME eidos_zlib) ++#file(GLOB_RECURSE ZLIB_SOURCES ${PROJECT_SOURCE_DIR}/eidos_zlib/*.c) ++#set(ZLIB_INCLUDES ${PROJECT_SOURCE_DIR}/eidos_zlib) ++#add_library(${TARGET_NAME} STATIC ${ZLIB_SOURCES}) ++#target_include_directories(${TARGET_NAME} PUBLIC) + + # KASTORE + set(TARGET_NAME kastore) +@@ -198,7 +200,7 @@ list(APPEND SLIM_SOURCES "${CMAKE_CURRENT_BINARY_DIR}/GitSHA1.cpp" ${PROJECT_SOU + + add_executable(${TARGET_NAME} ${SLIM_SOURCES}) + target_include_directories(${TARGET_NAME} PRIVATE ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/core" "${PROJECT_SOURCE_DIR}/eidos") +-target_link_libraries(${TARGET_NAME} PUBLIC gsl eidos_zlib tables) ++target_link_libraries(${TARGET_NAME} PUBLIC gsl gslcblas z tables) + if(WIN32) + set_source_files_properties(${SLIM_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h") + set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib") +@@ -211,7 +213,7 @@ set(TARGET_NAME eidos) + file(GLOB_RECURSE EIDOS_SOURCES ${PROJECT_SOURCE_DIR}/eidos/*.cpp ${PROJECT_SOURCE_DIR}/eidostool/*.cpp) + add_executable(${TARGET_NAME} ${EIDOS_SOURCES}) + target_include_directories(${TARGET_NAME} PRIVATE ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/eidos") +-target_link_libraries(${TARGET_NAME} PUBLIC gsl eidos_zlib tables) ++target_link_libraries(${TARGET_NAME} PUBLIC gsl gslcblas z tables) + if(WIN32) + set_source_files_properties(${EIDOS_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h") + set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim eidos PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib") +@@ -244,15 +246,15 @@ set_target_properties( ${TARGET_NAME} PROPERTIES LINKER_LANGUAGE CXX) + target_compile_definitions( ${TARGET_NAME} PRIVATE EIDOSGUI=1 SLIMGUI=1) + target_include_directories(${TARGET_NAME} PUBLIC ${GSL_INCLUDES} "${PROJECT_SOURCE_DIR}/QtSLiM" "${PROJECT_SOURCE_DIR}/eidos" "${PROJECT_SOURCE_DIR}/core" "${PROJECT_SOURCE_DIR}/treerec" "${PROJECT_SOURCE_DIR}/treerec/tskit/kastore") + if(APPLE) +- target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib /usr/lib/libobjc.A.dylib ) ++ target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z /usr/lib/libobjc.A.dylib ) + else() + if(WIN32) + set_source_files_properties(${QTSLIM_SOURCES} PROPERTIES COMPILE_FLAGS "-include config.h") + set_source_files_properties(${GNULIB_NAMESPACE_SOURCES} TARGET_DIRECTORY slim eidos SLiMgui PROPERTIES COMPILE_FLAGS "-include config.h -DGNULIB_NAMESPACE=gnulib") + target_include_directories(${TARGET_NAME} BEFORE PUBLIC ${GNU_DIR}) +- target_link_libraries(${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib gnu ) ++ target_link_libraries(${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z gnu ) + else() +- target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl tables eidos_zlib ) ++ target_link_libraries( ${TARGET_NAME} PUBLIC Qt5::Widgets Qt5::Core Qt5::Gui OpenGL::GL gsl gslcblas tables z ) + endif() + endif() + install(TARGETS ${TARGET_NAME} DESTINATION bin) +diff --git a/eidos/eidos_functions.cpp b/eidos/eidos_functions.cpp +index 4f52c763..ac9de199 100644 +--- a/eidos/eidos_functions.cpp ++++ b/eidos/eidos_functions.cpp +@@ -55,11 +55,11 @@ + + #include "string.h" + +-#include "gsl_linalg.h" +-#include "gsl_errno.h" +-#include "gsl_cdf.h" ++#include ++#include ++#include + +-#include "../eidos_zlib/zlib.h" ++#include + + #include "eidos_globals.h" + #if EIDOS_ROBIN_HOOD_HASHING +@@ -11475,7 +11475,7 @@ EidosValue_SP Eidos_ExecuteFunction_writeTempFile(const std::vector + + // for Eidos_calc_sha_256() + #include + + // for _Eidos_FlushZipBuffer() +-#include "../eidos_zlib/zlib.h" ++#include + + // for Eidos_ColorPaletteLookup() + #include "eidos_tinycolormap.h" +@@ -1570,7 +1570,7 @@ bool _Eidos_FlushZipBuffer(const std::string &file_path, const std::string &outs + { + //std::cout << "_Eidos_FlushZipBuffer() called for " << file_path << std::endl; + +- gzFile gzf = z_gzopen(file_path.c_str(), "ab"); ++ gzFile gzf = gzopen(file_path.c_str(), "ab"); + + if (!gzf) + return false; +@@ -1678,7 +1678,7 @@ void Eidos_WriteToFile(const std::string &p_file_path, std::vector ++#include + + #include + #include diff --git a/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb b/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb new file mode 100644 index 000000000000..d72d6e89e6ba --- /dev/null +++ b/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5-foss-2022a.eb @@ -0,0 +1,84 @@ +easyblock = 'PythonBundle' + +name = 'SMAP' +version = '4.6.5' + +homepage = 'https://ngs-smap.readthedocs.io' +description = "SMAP is an analysis tool for stack-based NGS read mapping" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Autotools', '20220317'), # required for isal +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # for pandas + ('matplotlib', '3.5.2'), + ('BEDTools', '2.30.0'), + ('pybedtools', '0.9.0'), + ('Pysam', '0.19.1'), + ('Biopython', '1.79'), + ('openpyxl', '3.0.10'), + ('plotly.py', '5.12.0'), +] + +use_pip = True + +exts_list = [ + ('setuptools', '67.6.1', { + 'checksums': ['257de92a9d50a60b8e22abfcbb771571fde0dbf3ec234463212027a4eeecbe9a'], + }), + ('colorlog', '6.7.0', { + 'checksums': ['bd94bd21c1e13fac7bd3153f4bc3a7dc0eb0974b8bc2fdf1a989e474f6e582e5'], + }), + ('primer3-py', '1.2.0', { + 'checksums': ['9e511e90987d4beda11f1f065b81805bc0c26a08084154e87fda46136ecf7518'], + 'modulename': 'primer3', + }), + ('dnaio', '0.10.0', { + 'checksums': ['de51a50948f00b864297d74eddb588fbee5ac229855754e77564d18b24619d18'], + }), + ('isal', '1.1.0', { + 'checksums': ['1364f4e3255a57d51c01422ab3ae785a43c076d516ebf49f6a25adecf8232105'], + }), + ('xopen', '1.7.0', { + 'checksums': ['901f9c8298e95ed74767a4bd76d9f4cf71d8de27b8cf296ac3e7bc1c11520d9f'], + }), + # smap-haplotype-window 1.8.1 requires cutadapt <= 4.1 (requires cutadapt.utils.reverse_complemented_sequence) + ('cutadapt', '4.1', { + 'checksums': ['be745ff24adfb4a3eaf715dfad0e2ccdfad7792ef00c1122adf4fbf3aed9227b'], + }), + ('ngs-smap', version, { + 'patches': ['SMAP-4.6.5_no-bin-bedtools.patch'], + 'checksums': [ + {'ngs-smap-4.6.5.tar.gz': 'bd6fd5a9fb5be66c5d21410376ed6b13eeb23da040c498d60dad6a8fb45d9d5e'}, + {'SMAP-4.6.5_no-bin-bedtools.patch': 'a43460694378628129d2cd3373e850fccb2ca330680f6fea3e31db9e4589d7ca'}, + ], + 'preinstallopts': "rm bin/bedtools && sed -i 's/~=/>=/g' setup.cfg && ", + 'modulename': 'smap', + }), + ('smap-haplotype-window', '1.8.1', { + 'checksums': ['5e244ecec8cb798d294014378c735dd2ab3d32f8266c7d161cf733099715fbbe'], + 'modulename': 'smap_window', + }), + ('gffpandas', '1.2.0', { + 'checksums': ['1a1e1c5c5120bf46ec57517222ebb42ffaab3f768c972fec54c4ac1b07b7f0c6'], + }), + ('smap-effect-prediction', '0.1.2', { + 'checksums': ['af16135eb3a2d9c22287a06d595010c46957711358734d73daaa21059ac27ca2'], + 'preinstallopts': "sed -i 's/~=/>=/g' setup.cfg && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/smap'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["smap compare --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5_no-bin-bedtools.patch b/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5_no-bin-bedtools.patch new file mode 100644 index 000000000000..a895ac74cab4 --- /dev/null +++ b/easybuild/easyconfigs/s/SMAP/SMAP-4.6.5_no-bin-bedtools.patch @@ -0,0 +1,15 @@ +don't install pre-compiled 'bedtools' binary, since BEDTools is provided as a proper dependency via EasyBuild +author: Kenneth Hoste (HPC-UGent) +--- ngs-smap-4.6.5/setup.cfg.orig 2022-10-11 09:59:22.522325500 +0200 ++++ ngs-smap-4.6.5/setup.cfg 2023-04-07 16:48:58.434620448 +0200 +@@ -49,10 +49,6 @@ + sphinx_rtd_theme~=1.0.0 + sphinx-tabs~=3.2.0 + +-[options.data_files] +-bin = +- bin/bedtools +- + [egg_info] + tag_build = + tag_date = 0 diff --git a/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-11.2.0.eb new file mode 100644 index 000000000000..ca3aa98f6b69 --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'SNAP' +version = '2.0.1' + +homepage = 'https://www.microsoft.com/en-us/research/project/snap' +description = """Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for + high-throughput sequencing data""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'cstd': 'c++98'} + +source_urls = ['https://github.com/amplab/snap/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['30f199c583e054c50ca6f3b61f27066640b7c829e5c5e8083841596a2869c064'] + +dependencies = [('zlib', '1.2.11')] + +buildopts = 'CXX="$CXX"' + +files_to_copy = [(['snap-aligner', 'SNAPCommand'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/snap-aligner', 'bin/SNAPCommand'], + 'dirs': [], +} + +sanity_check_commands = ["snap-aligner --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.2.0.eb b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.2.0.eb new file mode 100644 index 000000000000..2b1ee760c823 --- /dev/null +++ b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-12.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'SOCI' +version = '4.0.3' + +homepage = 'http://soci.sourceforge.net/' +description = """SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the + regular C++ code, staying entirely within the Standard C++.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/SOCI/soci/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4b1ff9c8545c5d802fbe06ee6cd2886630e5c03bf740e269bb625b45cf934928'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Boost', '1.81.0'), + ('SQLite', '3.39.4'), + ('PostgreSQL', '15.2'), +] + +# Matches RStudio (1.4.1717) install options +# https://github.com/rstudio/rstudio/blob/ddcd7191ec89c4da00e77afae7e9f27e61e87c36/dependencies/common/install-soci +configopts = "-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true " +configopts += "-DSOCI_TESTS=OFF " +configopts += "-DSOCI_CXX11=ON " +configopts += "-DSOCI_EMPTY=OFF " +configopts += '-DCMAKE_INCLUDE_PATH="$EBROOTBOOST/include" ' +configopts += "-DBoost_USE_STATIC_LIBS=ON " +configopts += '-DCMAKE_LIBRARY_PATH="$EBROOTBOOST/lib" ' +configopts += "-DWITH_BOOST=ON " +configopts += "-DWITH_POSTGRESQL=ON " +configopts += "-DWITH_SQLITE3=ON " +configopts += "-DWITH_DB2=OFF " +configopts += "-DWITH_MYSQL=OFF " +configopts += "-DWITH_ORACLE=OFF " +configopts += "-DWITH_FIREBIRD=OFF " +configopts += "-DWITH_ODBC=OFF " +configopts += "-DBoost_DEBUG=1 " + +local_dbs = ['postgresql', 'sqlite3'] + +sanity_check_paths = { + 'files': ['lib/libsoci_%s.%s' % (x, SHLIB_EXT) for x in local_dbs + ['core']], + 'dirs': ['include/soci/%s' % x for x in local_dbs], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.41.2-GCCcore-13.1.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.41.2-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..4ea12e5cf789 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.41.2-GCCcore-13.1.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.41.2' +local_filename_version = '3410200' + +homepage = 'https://www.sqlite.org/' +description = "SQLite: SQL Database Engine in a C Library" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.sqlite.org/2023/'] +sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] +checksums = ['e98c100dd1da4e30fa460761dab7c0b91a50b785e167f8c57acc46514fae9499'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('libreadline', '8.2'), + ('Tcl', '8.6.13'), +] + +# enable additional APIs that provide access to meta-data about tables and queries +# needed for GDAL when it used as a dep for QGIS +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"' + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +sanity_check_commands = [ + 'sqlite3 --version | grep ^%(version)s', +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.42.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.42.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..f3ebb9f775ee --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.42.0-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.42.0' +local_filename_version = '3420000' + +homepage = 'https://www.sqlite.org/' +description = "SQLite: SQL Database Engine in a C Library" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.sqlite.org/2023/'] +sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] +checksums = ['7abcfd161c6e2742ca5c6c0895d1f853c940f203304a0b49da4e1eca5d088ca6'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('libreadline', '8.2'), + ('Tcl', '8.6.13'), +] + +# enable additional APIs that provide access to meta-data about tables and queries +# needed for GDAL when it used as a dep for QGIS +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"' + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +sanity_check_commands = [ + 'sqlite3 --version | grep ^%(version)s', +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-11.2.0.eb new file mode 100644 index 000000000000..1eaefad2e9d9 --- /dev/null +++ b/easybuild/easyconfigs/s/SVG/SVG-2.87-GCC-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PerlModule' + +name = 'SVG' +version = '2.87' + +homepage = 'https://metacpan.org/pod/SVG' +description = "Perl binding for SVG" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR/'] +sources = [SOURCE_TAR_GZ] +checksums = ['b3fa58c1c59942b4ebef003da97c3e01e531480ca29e8efbe327ff0589c0bd3c'] + +dependencies = [ + ('Perl', '5.34.0'), +] + +options = {'modulename': 'SVG'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/SVG.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/SVG'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..5f49d35f2d68 --- /dev/null +++ b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.13-GCCcore-11.2.0.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'Scalene' +version = '1.5.13' + +homepage = 'https://github.com/plasma-umass/scalene' +description = """Scalene is a high-performance CPU, GPU and memory profiler for Python that does a number of things +that other Python profilers do not and cannot do. It runs orders of magnitude faster than other profilers while +delivering far more detailed information.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.0', { + 'checksums': ['3f4219469c55453cfe4737e564b67c2a149109dabf7f242478948b895f61106f'], + }), + ('pynvml', '11.4.1', { + 'checksums': ['b2e4a33b80569d093b513f5804db0c7f40cfc86f15a013ae7a8e99c5e175d5dd'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '12.6.0', { + 'checksums': ['ba3a3775974105c221d31141f2c116f4fd65c5ceb0698657a11e9f295ec93fd0'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['0077d517249cfa6ad0953d85c9656bdaca57b863159bbb78969987d9bdbb539c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/scalene'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["scalene --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb index f6d9d0f80459..9f60a08cff4a 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb @@ -51,12 +51,14 @@ exts_list = [ 'patches': [ 'scipy-1.10.1_disable-tests.patch', 'scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch', + 'scipy-1.10.1_fix-lobpcg-test.patch', ], 'checksums': [ {'scipy-1.10.1.tar.gz': '2cf9dfb80a7b4589ba4c40ce7588986d6d5cebc5457cad2c2880f6bc2d42f3a5'}, {'scipy-1.10.1_disable-tests.patch': '5d36d416fb7ea9297514c3988d9f506793e39dc4c0daedccf6733c3dd7e3dcc0'}, {'scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch': '48177d6af51cf3e3d46aed8425807f0a65a498f7558f475032e0ad846559a23e'}, + {'scipy-1.10.1_fix-lobpcg-test.patch': 'eb4c576959108df0b1749705e64fe42e79edcf5aa8f6b4d7908f9b136d0d6648'}, ], 'enable_slow_tests': True, 'ignore_test_result': False, diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch new file mode 100644 index 000000000000..45668de46ae3 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-lobpcg-test.patch @@ -0,0 +1,29 @@ +change test for a warning to filterwarnings since the code may or not issue a warning depending on an arch +see https://github.com/scipy/scipy/issues/17954 + https://github.com/scipy/scipy/pull/17975 +diff --git a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py +index afd7a106ea0..87f3756c37d 100644 +--- a/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py ++++ b/scipy/sparse/linalg/_eigen/lobpcg/tests/test_lobpcg.py +@@ -255,17 +255,18 @@ + _check_fiedler(12, 2) + + +-@pytest.mark.skipif(platform.machine() == 'aarch64', +- reason="issue #15935") ++@pytest.mark.filterwarnings("ignore:Failed at iteration") ++@pytest.mark.filterwarnings("ignore:Exited at iteration") ++@pytest.mark.filterwarnings("ignore:Exited postprocessing") + def test_failure_to_run_iterations(): + """Check that the code exists gracefully without breaking. Issue #10974. ++ The code may or not issue a warning, filtered out. Issue #15935, #17954. + """ + rnd = np.random.RandomState(0) + X = rnd.standard_normal((100, 10)) + A = X @ X.T + Q = rnd.standard_normal((X.shape[0], 4)) +- with pytest.warns(UserWarning, match="Failed at iteration"): +- eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12) ++ eigenvalues, _ = lobpcg(A, Q, maxiter=40, tol=1e-12) + assert(np.max(eigenvalues) > 0) + + diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.2-foss-2022b.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.2-foss-2022b.eb new file mode 100644 index 000000000000..ca9fa388cb0a --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.2-foss-2022b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.12.2' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['374645f36509d0dcab895cba5b47daf0586f77bfe3b36c97c607db7da5be0139'] + +dependencies = [ + ('Python', '3.10.8'), + ('matplotlib', '3.7.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb index be3f28cdb22c..0489f0e3fcfd 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.1-foss-2020b-R-4.0.3.eb @@ -9,37 +9,35 @@ description = "Seurat is an R package designed for QC, analysis, and exploration toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] - dependencies = [ ('R', '4.0.3'), ('R-bundle-Bioconductor', '3.12', versionsuffix), ] exts_defaultclass = 'RPackage' -exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} exts_list = [ ('spatstat.utils', '2.1-0', { - 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.utils'], 'checksums': ['ed3569fea295b62396c49cdcfe476414b0b0f3e52044175532f316a402d3f8a1'], }), ('spatstat.data', '2.1-0', { 'checksums': ['1b9840ad0ec7eddfa98a01e8b8a5291e5cb447c3082aa7d7b4df762577f95533'], }), ('spatstat.geom', '2.0-1', { - 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.geom'], 'checksums': ['70ebfe115e733b2e6778baf6e2935861472154c0dd21f15a84ec2a61e0a3f6e4'], }), ('spatstat.sparse', '2.0-0', { 'checksums': ['27fbce64e21f095a5e9ac54c86f91c9f4b45eac3c2358580e04423b4beba19c7'], }), ('spatstat.core', '2.0-0', { - 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.core'], 'checksums': ['fde9a91bd32b7a3c8b25e802a16d470dcc919c24da5715149e1d91eeec119ba7'], }), (name, version, { diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb index d71472a2d5ea..b8a228157b70 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.0.3-foss-2020b-R-4.0.3.eb @@ -9,19 +9,20 @@ description = "Seurat is an R package designed for QC, analysis, and exploration toolchain = {'name': 'foss', 'version': '2020b'} -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] - dependencies = [ ('R', '4.0.3'), ('R-bundle-Bioconductor', '3.12', versionsuffix), ] exts_defaultclass = 'RPackage' -exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} exts_list = [ ('spatstat.utils', '2.2-0', { @@ -31,14 +32,12 @@ exts_list = [ 'checksums': ['1b9840ad0ec7eddfa98a01e8b8a5291e5cb447c3082aa7d7b4df762577f95533'], }), ('spatstat.geom', '2.2-0', { - 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.geom'], 'checksums': ['70b063a7f317f531b2afb3afaedb047fce81b39ee481a4067962529d6069634c'], }), ('spatstat.sparse', '2.0-0', { 'checksums': ['27fbce64e21f095a5e9ac54c86f91c9f4b45eac3c2358580e04423b4beba19c7'], }), ('spatstat.core', '2.2-0', { - 'source_urls': ['https://cran.r-project.org/src/contrib/Archive/spatstat.core'], 'checksums': ['0ecbc1ae688c8d4f41db3efa6253ac8db5c432ef714240d01a2b195950d65253'], }), ('Matrix', '1.3-4', { diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb index af03c5702855..19cfccaecdcb 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb @@ -9,19 +9,20 @@ description = "Seurat is an R package designed for QC, analysis, and exploration toolchain = {'name': 'foss', 'version': '2022a'} -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] - dependencies = [ ('R', '4.2.1'), ('R-bundle-Bioconductor', '3.15', versionsuffix), ] exts_defaultclass = 'RPackage' -exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} exts_list = [ ('Matrix', '1.5-1', { diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb index b98250be5b35..fe25468c3f6c 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb @@ -9,19 +9,20 @@ description = "Seurat is an R package designed for QC, analysis, and exploration toolchain = {'name': 'foss', 'version': '2021b'} -source_urls = [ - 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'https://cran.r-project.org/src/contrib/', # current version of packages - 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages -] - dependencies = [ ('R', '4.1.2'), ('R-bundle-Bioconductor', '3.14', versionsuffix), ] exts_defaultclass = 'RPackage' -exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} exts_list = [ ('Matrix', '1.5-3', { diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 000000000000..032d6c672cdc --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,73 @@ +easyblock = 'Bundle' + +name = 'Seurat' +version = '4.3.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://satijalab.org/seurat' +description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} + +exts_list = [ + ('Matrix', '1.5-4', { + 'checksums': ['15ceb61993d61b442068104abb46e6d91b5a1179c01eeb64563b853abab66f06'], + }), + ('sp', '1.5-1', { + 'checksums': ['69b9eab481d389bbb736d2adcf50c180aca248c3ffc4ebda8ffe2accc5f229df'], + }), + ('SeuratObject', '4.1.3', { + 'checksums': ['585d2754f6165a367f0f458523f0a25d4d4160c929c931b27c5603cc6bd986d3'], + }), + ('sctransform', '0.3.5', { + 'checksums': ['c08e56df05d64ed04ee53eb9e1d4d321da8aff945e36d56db1d5ceb1cd7e6e0b'], + }), + ('uwot', '0.1.14', { + 'checksums': ['8016e8192b7e72604ca71840cbe43fa1d2caed8a8ad7cbf20e85cd3b384a9fe0'], + }), + ('spatstat.utils', '3.0-1', { + 'checksums': ['cba1c7806564fd9145ca15edf77233d6ba5609f0989f7812221f5fc1ece0b91a'], + }), + ('spatstat.data', '3.0-0', { + 'checksums': ['cff9058a88489020a4a05b9576cd452f37fa9b42084873c474d06931f5187057'], + }), + ('spatstat.geom', '3.0-3', { + 'checksums': ['6e5b56c60e774a0cdcaa5a8ffde071225f233832446a341588bd8a7840913c84'], + }), + ('spatstat.random', '3.0-1', { + 'checksums': ['938c845c063b8781bf894c0a67537e7b2a7c425a4beba4a95ec9d2c37b43e5b6'], + }), + ('spatstat.sparse', '3.0-0', { + 'checksums': ['99be0a3c7592760fdf1668dc0811f75ed91c400390d1ecc3d5e643255f501ad2'], + }), + ('spatstat.explore', '3.0-5', { + 'checksums': ['9f438a12fac3f3e1d0bd550b1393c1e5732be694517b0878db09da557d6dc862'], + }), + (name, version, { + 'checksums': ['7ebacb3b86f74279de60b597f9a6e728f0668719811b0dca3425d21762fff97c'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2022b.eb b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2022b.eb new file mode 100644 index 000000000000..ab2fa48ba51f --- /dev/null +++ b/easybuild/easyconfigs/s/Shapely/Shapely-2.0.1-foss-2022b.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonPackage' + +name = 'Shapely' +version = '2.0.1' + +homepage = 'https://github.com/Toblerity/Shapely' +description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. +It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['66a6b1a3e72ece97fc85536a281476f9b7794de2e646ca8a4517e2e3c1446893'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('GEOS', '3.11.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.5.0-foss-2022a.eb b/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.5.0-foss-2022a.eb new file mode 100644 index 000000000000..494b3757f7bb --- /dev/null +++ b/easybuild/easyconfigs/s/ShengBTE/ShengBTE-1.5.0-foss-2022a.eb @@ -0,0 +1,43 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'ShengBTE' +version = '1.5.0' + +homepage = 'https://bitbucket.org/sousaw/shengbte' +description = "A solver for the Boltzmann transport equation for phonons." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True} + +bitbucket_account = 'sousaw' +source_urls = [BITBUCKET_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['fc1299921aa5f8046473d0c73114b826f803650b9a44e94338eaeb13e9c67381'] + +dependencies = [ + ('spglib', '2.0.2'), +] + +start_dir = 'Src' + +# strip "include arch.make" -- not needed as we already set necessary env vars +prebuildopts = "sed -i 's/^include arch.make//' Makefile && " +# -fallow-argument-mismatch needed for GCC 10+ +buildopts = '-j 1 LIBS="$LIBBLAS -lsymspg" FFLAGS="$FFLAGS -fallow-argument-mismatch"' + +local_tests = ["Test-%s" % x for x in ['QE', 'RTA', 'VASP']] + +files_to_copy = [([name], 'bin'), (['LICENSE', 'README.md'], 'share')] + local_tests + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['share'] + local_tests, +} + +sanity_check_commands = [ + "cd %%(builddir)s/*%%(namelower)s*/%s && %%(mpi_cmd_prefix)s %%(name)s" % x for x in local_tests +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb new file mode 100644 index 000000000000..b2f900f3c4aa --- /dev/null +++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2021b-fast.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'PythonPackage' + +name = 'SignalP' +version = '6.0g' +_suffix = 'fast' +versionsuffix = '-' + _suffix + +homepage = 'https://services.healthtech.dtu.dk/software.php' +description = """SignalP predicts the presence and location of signal peptide cleavage sites +in amino acid sequences from different organisms""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +download_instructions = """ +SignalP requires registration and acceptance of licence terms (academic use only). + [1] go to: https://services.healthtech.dtu.dk/service.php?SignalP-6.0 + [2] navigate to the "Downloads" tab + [3] select "%s" type under version "%%(version)s" + [4] complete the form; you should receive a download link via email +""" % _suffix + +sources = ['%%(namelower)s-%%(version)s.%s.tar.gz' % _suffix] +unpack_options = '--strip-components=1' +checksums = ['a16fcea2b30067d2622d446031978bd86927e2e1cecf29a567c7922f6861b5aa'] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # numpy > 1.19.2 + ('tqdm', '4.62.3'), # tqdm > 4.46.1 + ('PyTorch', '1.12.1'), # torch > 1.7.0 + ('matplotlib', '3.4.3'), # matplotlib > 3.3.2 +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +_bin = '%%(namelower)s%s' % version[0] +sanity_check_paths = { + 'files': ['bin/%s' % _bin], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%s --help' % _bin] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb new file mode 100644 index 000000000000..f2575df86914 --- /dev/null +++ b/easybuild/easyconfigs/s/Simple-DFTD3/Simple-DFTD3-0.7.0-foss-2022a.eb @@ -0,0 +1,48 @@ +# A. Domingo (Vrije Universiteit Brussel) +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'Simple-DFTD3' +version = '0.7.0' + +homepage = 'https://dftd3.readthedocs.io' +description = """Reimplementation of the D3 dispersion correction. The s-dftd3 project aims to +provide a user-friendly and uniform interface to the D3 dispersion model and +for the calculation of DFT-D3 dispersion corrections.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': False, 'openmp': True, 'pic': True} + +github_account = 'dftd3' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['19400a176eb4dcee7b89181a5a5f0033fe6b05c52821e54896a98448761d003a'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.2.0'), + ('TOML-Fortran', '0.3.1'), +] + +build_shared_libs = True + +configopts = '-DWITH_BLAS=1 -DWITH_OpenMP=1' + +# run suite of tests with ctest +test_cmd = 'ctest' +runtest = '' + +sanity_check_paths = { + 'files': ['bin/s-dftd3', 'lib/libs-dftd3.%s' % SHLIB_EXT, 'include/dftd3.h', 'include/s-dftd3.h'], + 'dirs': ['include/s-dftd3', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["s-dftd3 --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/SoPlex/SoPlex-2.2.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SoPlex/SoPlex-2.2.1-GCC-11.3.0.eb new file mode 100644 index 000000000000..309841532c74 --- /dev/null +++ b/easybuild/easyconfigs/s/SoPlex/SoPlex-2.2.1-GCC-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'SoPlex' +version = '2.2.1' + +homepage = 'https://soplex.zib.de/' +description = """SoPlex is an optimization package for solving linear programming problems (LPs) +based on an advanced implementation of the primal and dual revised simplex +algorithm. It provides special support for the exact solution of LPs with +rational input data. It can be used as a standalone solver reading MPS or LP +format files via a command line interface as well as embedded into other +programs via a C++ class library.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'scipopt' +source_urls = [GITHUB_SOURCE] +sources = ['release-%s.tar.gz' % version.replace('.', '')] +checksums = ['6c2e89cd7c8910f8989f2a860fa0446641bd16d76eb87872f70974838486c9b1'] + +dependencies = [ + ('GMP', '6.2.1'), + ('zlib', '1.2.12'), +] + +skipsteps = ['configure'] + +buildopts = "COMP=gnu OPT=opt" +installopts = "INSTALLDIR=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/soplex', 'lib/libsoplex.a'], + 'dirs': ['include'], +} + +sanity_check_commands = ["soplex | grep -q '%(name)s version %(version)s'"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SoupX/SoupX-1.6.2-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/SoupX/SoupX-1.6.2-foss-2022a-R-4.2.1.eb new file mode 100644 index 000000000000..3354780d23e2 --- /dev/null +++ b/easybuild/easyconfigs/s/SoupX/SoupX-1.6.2-foss-2022a-R-4.2.1.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'SoupX' +version = '1.6.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/constantAmateur/SoupX' +description = """" +Quantify, profile and remove ambient mRNA contamination (the "soup") from +droplet based single cell RNA-seq experiments. Implements the method described +in Young et al. (2018) .""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://cran.r-project.org/src/contrib/'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['9b6226cd7c0691498a874d5c029f8ff81fd2060295c298985397521c1f7ee3a5'] + +dependencies = [ + ('R', '4.2.1'), + ('Seurat', '4.3.0', versionsuffix) +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Structure/Structure-2.3.4-GCC-12.2.0.eb b/easybuild/easyconfigs/s/Structure/Structure-2.3.4-GCC-12.2.0.eb new file mode 100644 index 000000000000..94412d6b87ae --- /dev/null +++ b/easybuild/easyconfigs/s/Structure/Structure-2.3.4-GCC-12.2.0.eb @@ -0,0 +1,41 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'Structure' +version = '2.3.4' + +homepage = 'https://web.stanford.edu/group/pritchardlab/structure.html' +description = """The program structure is a free software package for using multi-locus genotype data to investigate + population structure.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v%(version)s/'] +sources = [{'download_filename': 'structure_kernel_source.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['f2b72b9189a514f53e921bbdc1aa3dbaca7ac34a8467af1f972c7e4fc9c0bb37'] + +# Add -fcommon to fix "multiple definition" errors +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon" && ' +buildopts = 'all CC="$CC" OPT="$CFLAGS"' + +files_to_copy = [(['structure'], 'bin')] + +sanity_check_commands = [ + 'structure | grep "Version %(version)s"' +] + +sanity_check_paths = { + 'files': ['bin/structure'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Subread/Subread-2.0.4-GCC-11.3.0.eb b/easybuild/easyconfigs/s/Subread/Subread-2.0.4-GCC-11.3.0.eb new file mode 100644 index 000000000000..27bc601b2e93 --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-2.0.4-GCC-11.3.0.eb @@ -0,0 +1,39 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'MakeCp' + +name = 'Subread' +version = '2.0.4' + +homepage = 'https://subread.sourceforge.net/' +description = """High performance read alignment, quantification and mutation discovery""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +checksums = ['c54b37ed83b34318d8f119b5c02fb9d0a65c811195bcc9e1745df6daf74ca2db'] + +start_dir = 'src' + +prebuildopts = "sed -i 's/-mtune=core2//g' Makefile.Linux && " +prebuildopts += "sed -i 's/-mtune=core2//g' longread-one/Makefile && " + +buildopts = " -f Makefile.Linux" + +files_to_copy = ['bin'] + +local_binaries_list = [ + 'exactSNP', 'featureCounts', 'subindel', 'subjunc', 'sublong', '%(namelower)s-align', '%(namelower)s-buildindex', +] +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_binaries_list], + 'dirs': ['bin/utilities'], +} + +sanity_check_commands = [ + 'cd %(builddir)s/%(namelower)s-%(version)s-source/test && bash test_all.sh' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb new file mode 100644 index 000000000000..810a3aa16d00 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021a-METIS-5.1.0.eb @@ -0,0 +1,39 @@ +name = 'SuiteSparse' +version = '5.10.1' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2021a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'SuiteSparse_disable-qopt-report.patch', +] +checksums = [ + {'v5.10.1.tar.gz': 'acb4d1045f48a237e70294b950153e48dce5b5f9ca8190e86c2b8c54ce00a7ee'}, + {'SuiteSparse_disable-qopt-report.patch': 'f96bcd993f4dd90a70aedcb2901582ac99f449ac359b46a36190862a16aeb870'}, +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('M4', '1.4.18'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.1.0'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " +# The default way to do a parallel make won't work with the Makefiles for +# SuiteSparse, JOBS has to be set to the desired parallelism +parallel = 1 +prebuildopts += "export JOBS=4 && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb new file mode 100644 index 000000000000..ade731aac571 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.10.1-intel-2021b-METIS-5.1.0.eb @@ -0,0 +1,31 @@ +name = 'SuiteSparse' +version = '5.10.1' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['acb4d1045f48a237e70294b950153e48dce5b5f9ca8190e86c2b8c54ce00a7ee'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.1.0'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " +# disable optimisation report to reduce memory use during compile +prebuildopts += 'sed -i "s/-qopt-report=5/-qopt-report=0/" GraphBLAS/CMakeLists.txt && ' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse_disable-qopt-report.patch b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse_disable-qopt-report.patch new file mode 100644 index 000000000000..db00fb87ea12 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse_disable-qopt-report.patch @@ -0,0 +1,14 @@ +Compiling GraphBLAS with the intel toolchain consumes *a lot* of memory +because optimization reports are generated. This patch simply turns that off +to make the memory requirement for compilation more sensible. +--- GraphBLAS/CMakeLists.txt.orig 2023-03-17 14:46:24.533943000 +0100 ++++ GraphBLAS/CMakeLists.txt 2023-03-17 14:46:15.393912000 +0100 +@@ -198,7 +198,7 @@ + elseif ( "${CMAKE_C_COMPILER_ID}" STREQUAL "Intel" ) + # options for icc: also needs -std=c11 + set ( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -diag-disable 10397,15552 " ) +- set ( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -qopt-report=5 -qopt-report-phase=vec" ) ++ set ( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -qopt-report=0 -qopt-report-phase=vec" ) + # the -mp1 option is important for predictable floating-point results with + # the icc compiler. Without, ((float) 1.)/((float) 0.) produces NaN, + # instead of the correct result, Inf. diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..e0a01221b9d0 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1.1' + +homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' + +description = """ + Szip compression software, providing lossless compression of scientific data +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/sceasy/sceasy-0.0.7-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/sceasy/sceasy-0.0.7-foss-2022a-R-4.2.1.eb new file mode 100644 index 000000000000..b20476c22ccd --- /dev/null +++ b/easybuild/easyconfigs/s/sceasy/sceasy-0.0.7-foss-2022a-R-4.2.1.eb @@ -0,0 +1,34 @@ +easyblock = 'RPackage' + +name = 'sceasy' +version = '0.0.7' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/cellgeni/sceasy' +description = "sceasy is a package that helps easy conversion of different single-cell data formats to each other" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/cellgeni/sceasy/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['bc6a2dba2111067f3247ff1ee617cc85ab6c7d89950f7d8ca486a3e34b27f9d6'] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), + ('Seurat', '4.3.0', versionsuffix), + ('anndata', '0.8.0'), + ('loompy', '3.0.7'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +sanity_check_commands = [ + """echo "library(reticulate); reticulate::import('anndata');" | R -q --no-save""", + """echo "library(reticulate); reticulate::import('loompy');" | R -q --no-save""", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scib/scib-1.1.3-foss-2021a.eb b/easybuild/easyconfigs/s/scib/scib-1.1.3-foss-2021a.eb new file mode 100644 index 000000000000..ffd4fc238c0d --- /dev/null +++ b/easybuild/easyconfigs/s/scib/scib-1.1.3-foss-2021a.eb @@ -0,0 +1,39 @@ +# author: Denis Kristak (INUITS) +easyblock = 'PythonPackage' + +name = 'scib' +version = '1.1.3' + +homepage = 'https://github.com/theislab/scib' +description = "Benchmarking atlas-level data integration in single-cell genomics." + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2b59d7c291e99bd508b91d73ff07fc4961fded37b06089e4f19fc5ee9cc4e3f3'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Seaborn', '0.11.2'), + ('numba', '0.53.1'), + ('scanpy', '1.8.1'), + ('h5py', '3.2.1'), + ('scikit-learn', '0.24.2'), + ('scikit-misc', '0.1.4'), + ('leidenalg', '0.8.7'), + ('umap-learn', '0.5.3'), + ('pydot', '1.4.2'), + ('igraph', '0.9.4'), + ('python-igraph', '0.9.6'), + ('Deprecated', '1.2.13'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +preinstallopts = "sed -i 's|igraph>=0.10|python-igraph>=0.9.6|g' setup.cfg && " +preinstallopts += "sed -i 's|louvain>=0.8||g' setup.cfg && " + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.2-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..ed4f8e89aff9 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build/scikit-build-0.17.2-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build' +version = '0.17.2' + +homepage = 'https://scikit-build.readthedocs.io/en/latest' +description = """Scikit-Build, or skbuild, is an improved build system generator +for CPython C/C++/Fortran/Cython extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('distro', '1.8.0', { + 'checksums': ['02e111d1dc6a50abb8eed6bf31c3e48ed8b0830d1ea2a1b78c61765c2513fdd8'], + }), + ('scikit_build', version, { + 'modulename': 'skbuild', + 'checksums': ['348cfd2137c68cbf9fa589ed74fd07b0340a65a1888e2481cfc63356485188a6'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.3.0.eb b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.3.0.eb new file mode 100644 index 000000000000..165375a4e100 --- /dev/null +++ b/easybuild/easyconfigs/s/seqtk/seqtk-1.3-GCC-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'seqtk' +version = '1.3' + +homepage = 'https://github.com/lh3/seqtk/' +description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. + It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5a1687d65690f2f7fa3f998d47c3c5037e792f17ce119dab52fff3cfdca1e563'] + +dependencies = [('zlib', '1.2.12')] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' + +preinstallopts = "mkdir %(installdir)s/bin && " +installopts = 'BINDIR=%(installdir)s/bin/' + +sanity_check_paths = { + 'files': ['bin/seqtk'], + 'dirs': [], +} + +sanity_check_commands = ["seqtk 2>&1 | grep 'Usage:[ ]*seqtk'"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb new file mode 100644 index 000000000000..6e5bfbf74c39 --- /dev/null +++ b/easybuild/easyconfigs/s/skorch/skorch-0.11.0-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'skorch' +version = '0.11.0' +local_pt_version = '1.10.0' +versionsuffix = '-PyTorch-%s-CUDA-%%(cudaver)s' % local_pt_version + +homepage = 'https://skorch.readthedocs.io/' +description = "A scikit-learn compatible neural network library that wraps PyTorch." + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b35cb4e50045742f0ffcfad33044af691d5d36b50212573753a804483a947ca9'] + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('scikit-learn', '0.24.2'), + ('tqdm', '4.61.2'), + ('PyTorch', local_pt_version, '-CUDA-%(cudaver)s'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..a221f9f9ea5a --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'snappy' +version = '1.1.10' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/google/snappy/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-1.1.9_use-default-rtti.patch', +] +checksums = [ + {'1.1.10.tar.gz': '49d831bffcc5f3d01482340fe5af59852ca2fe76c3e05df0e67203ebbe0f1d90'}, + {'snappy-1.1.9_use-default-rtti.patch': 'af56538330b2d781677c7d94576c15fc36e004ae0b4f1ac7d86bbec22b65e73d'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +# Disable building tests and benchmarks - we're not using them and they require googletest and benchmark source code +_configopts = '-DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF' +configopts = ['%s' % _configopts, '-DBUILD_SHARED_LIBS=ON %s' % _configopts] + +sanity_check_paths = { + 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..37e99e711245 --- /dev/null +++ b/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'spdlog' +version = '1.11.0' + +homepage = 'https://github.com/gabime/spdlog' +description = 'Very fast, header-only/compiled, C++ logging library.' +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/gabime/spdlog/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ca5cae8d6cac15dae0ec63b21d6ad3530070650f68076f3a4a862ca293a858bb'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['include/spdlog/spdlog.h'], + 'dirs': ['lib64/cmake', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..72f5f9a9923e --- /dev/null +++ b/easybuild/easyconfigs/s/spdlog/spdlog-1.11.0-GCCcore-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'spdlog' +version = '1.11.0' + +homepage = 'https://github.com/gabime/spdlog' +description = 'Very fast, header-only/compiled, C++ logging library.' +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/gabime/spdlog/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ca5cae8d6cac15dae0ec63b21d6ad3530070650f68076f3a4a862ca293a858bb'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['include/spdlog/spdlog.h'], + 'dirs': ['lib64/cmake', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 000000000000..e5b551b446f4 --- /dev/null +++ b/easybuild/easyconfigs/s/spektral/spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,37 @@ +# easybuild easyconfig +# +# John Dey +# +# Fred Hutchinson Cancer Center - Seattle Washington - US +# +easyblock = 'PythonPackage' + +name = 'spektral' +version = '1.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/danielegrattarola/spektral' +description = """Spektral is a Python library for graph deep learning. The main goal of this + project is to provide a simple but flexible framework for creating graph neural networks (GNNs).""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3b73549f213f0d36a0bf67595aa3c4d84efb8e0e40d71aeaa1d78ea896245222'] + +dependencies = [ + ('Python', '3.9.6'), + ('lxml', '4.6.3'), + ('SciPy-bundle', '2021.10'), + ('networkx', '2.6.3'), + ('tqdm', '4.62.3'), + ('scikit-learn', '1.0.1'), + ('CUDA', '11.4.1', '', SYSTEM), + ('TensorFlow', '2.7.1', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.2-gfbf-2022b.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.2-gfbf-2022b.eb new file mode 100644 index 000000000000..76b889951436 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.0.2-gfbf-2022b.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '2.0.2' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = "Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C." + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['1d081ec22da4ab4fc3198e9445ddad6dec2261c43927831151d93e39422610aa'] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/spglib/spglib-2.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/spglib/spglib-2.0.2-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..256f29f77b51 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-2.0.2-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'spglib' +version = '2.0.2' + +homepage = 'https://spglib.github.io/spglib/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/spglib/spglib/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['10e44a35099a0a5d0fc6ee0cdb39d472c23cb98b1f5167c0e2b08f6069f3db1e'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +postinstallcmds = ["cd %(installdir)s/include && mkdir spglib && ln -s ../spglib.h spglib/"] + +sanity_check_paths = { + 'files': [ + 'include/spglib.h', + 'lib/libsymspg.a', + 'lib/libsymspg.%s' % SHLIB_EXT + ], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb new file mode 100644 index 000000000000..2d2a1ab0f5da --- /dev/null +++ b/easybuild/easyconfigs/s/synthcity/synthcity-0.2.4-foss-2022a.eb @@ -0,0 +1,167 @@ +easyblock = 'PythonBundle' + +name = 'synthcity' +version = '0.2.4' + +local_pytorch_version = '1.12.0' + +homepage = 'https://github.com/vanderschaarlab/synthcity' +description = """A library for generating and evaluating synthetic tabular data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('lifelines', '0.27.4'), + ('SciPy-bundle', '2022.05'), + ('pydantic', '1.10.4'), + ('Redis', '7.0.8'), + ('scikit-learn', '1.1.2'), + ('SHAP', '0.41.0'), + ('PyTorch', local_pytorch_version), + ('XGBoost', '1.7.2'), + ('tqdm', '4.64.0'), + ('Mako', '1.2.0'), + ('PyYAML', '6.0'), + ('fastai', '2.7.10'), + ('h5py', '3.7.0'), + ('networkx', '2.8.4'), + ('protobuf', '3.19.4'), + ('Arrow', '8.0.0'), + ('pybind11', '2.9.2'), + ('PyTorch-Lightning', '1.8.4'), + ('spaCy', '3.4.4'), + ('tensorboard', '2.10.0'), + ('torchvision', '0.13.1'), + ('Brotli-python', '1.0.9'), + ('statsmodels', '0.13.1'), + ('imbalanced-learn', '0.10.1'), + ('Greenlet', '2.0.2'), + ('Optuna', '3.1.0'), + ('Cython', '0.29.33'), + ('cython-blis', '0.9.1'), + ('torchtext', '0.14.1', '-PyTorch-%s' % local_pytorch_version), + ('IPython', '8.5.0'), + ('MONAI', '1.0.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('decaf_synthetic_data', '0.1.6', { + 'modulename': 'decaf', + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['dc51502f9f72b3fbdbef697238d72ae6b8457f76efc9763a747970ba543d4e0f'], + }), + ('feather-format', '0.4.1', { + 'modulename': 'feather', + 'checksums': ['45f67e3745d394d4f160ca6d636bbfd4f8b68d01199dc1649b6e487d3e878903'], + }), + ('fflows', '0.0.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['18de7a7b98e3708ff2d5ae9f10fad625740230c4de6447906b7ca477667b78fb'], + }), + ('fsspec', '2022.7.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['36c5a8e7c4fc20cf32ef6934ac0a122accc8a593ddc8478d30c3ca4dbbd95500'], + }), + ('functorch', '0.2.0', { + 'source_urls': ['https://github.com/pytorch/%(name)s/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['ea6446b60d5e0847140e1a0dcb91d8a7de2b5844bba7c3f7560eb5020a05881f'], + }), + ('geomloss', '0.2.5', { + 'checksums': ['dcd851cc3c9625f384d4c18d235a790821162c34a2be503a61966b355b98456e'], + }), + ('inflate64', '0.3.1', { + 'checksums': ['b52dd8fefd2ba179e5dfa18d6eca7e2fc822584616271c039d5ef1f9ca90c71c'], + }), + ('keopscore', '2.1.1', { + 'checksums': ['07b4d254a28a9d4a43153663856677263dd7112912efacbad83c2a76ea0836f0'], + }), + ('loguru', '0.6.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['4e2414d534a2ab57573365b3e6d0234dfb1d84b68b7f3b948e6fb743860a77c3'], + }), + ('multivolumefile', '0.2.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['237f4353b60af1703087cf7725755a1f6fcaeeea48421e1896940cd1c920d678'], + }), + ('nflows', '0.14', { + 'checksums': ['6299844a62f9999fcdf2d95cb2d01c091a50136bd17826e303aba646b2d11b55'], + }), + ('opacus', '1.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ef5d6f2aab56901d714ee56fd177a3627d14d820b2ec49cb8bc8a6f52c326507'], + }), + ('opt_einsum', '3.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['2455e59e3947d3c275477df7f5205b30635e266fe6dc300e3d9f9646bfcea147'], + }), + ('pgmpy', '0.1.21', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['3c442320e7822892813b4eb56e048729d3bde053a707b5bb032685af6b372246'], + }), + ('py7zr', '0.20.4', { + 'checksums': ['1d01f98ea1e1f5c49940358691b2076f9a5848056426541e783de33834f59e21'], + }), + ('pybcj', '1.0.1', { + 'modulename': 'bcj', + 'checksums': ['8b682ed08caabfb7c042d4be083e28ddc692afb1deff5567111f8855071b75c3'], + }), + ('pycox', '0.2.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['9ea3c64a4a650ccf6c96cf512712de330f2d75de32122d86995c7cd37ff105d1'], + }), + ('pycryptodomex', '3.17', { + 'modulename': 'Crypto', + 'checksums': ['0af93aad8d62e810247beedef0261c148790c52f3cd33643791cc6396dd217c1'], + }), + ('pykeops', '2.1.1', { + 'checksums': ['1931823c746345ce5a5805adad6baa1add772c6fe1800375f7f9a3ddb38b6f71'], + }), + ('pyppmd', '1.0.0', { + 'checksums': ['075c9bd297e3b0a87dd7aeabca7fee668218acbe69ecc1c6511064558de8840f'], + }), + ('pyts', '0.12.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['acd66b0cf1fd17d9ce6449335f5da30701f65fdee185d4b918726b62ca6af79d'], + }), + ('pyzstd', '0.15.4', { + 'checksums': ['de07ac54f57642f186732075cdce2be3d4a30228c3b17a6d8c6053765dc6eec8'], + }), + ('texttable', '1.6.7', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['b7b68139aa8a6339d2c320ca8b1dc42d13a7831a346b446cb9eb385f0c76310c'], + }), + ('thinc', '8.1.9', { + 'checksums': ['8a1e65529c6d0796271d2a7e5ca6ea013fcb7dad69ec609d5093a25808107f51'], + # we are using blis 0.9.1 + # thinc has problems with blis>0.8.0 on Windows only (https://github.com/explosion/thinc/pull/772) + 'preinstallopts': 'sed -i "s/blis>=0.7.8,<0.8.0/blis>=0.7.8/g" setup.cfg && ', + }), + ('torchtuples', '0.2.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['186625230a149cc09f64116d51b203ffefe78160f5a0445adad195893663f55b'], + }), + ('tsai', '0.3.5', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['f5b888f7b968d1826a74eab3b8fa9559c6985d8532c017a4d85809e6c8e6cadd'], + }), + ('xgbse', '0.2.3', { + 'source_urls': ['https://github.com/loft-br/xgboost-survival-embeddings/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['9e6b71539b2b533c00eddfe7681cdd541f393d9573594eca358d263b141c127d'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['424448d420331743458bf63558a06a5fbefbad19392718cd0a755d4a4878476c'], + }), +] + +sanity_check_commands = [ + "python -c 'from synthcity.plugins import Plugins'", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb b/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb new file mode 100644 index 000000000000..8634f5e8d18f --- /dev/null +++ b/easybuild/easyconfigs/s/sysbench/sysbench-1.0.20-GCC-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'sysbench' +version = '1.0.20' + +homepage = 'https://github.com/akopytov/sysbench' +description = """sysbench is a scriptable multi-threaded benchmark tool based on LuaJIT. + It is most frequently used for database benchmarks, but can also be used to create arbitrarily complex + workloads that do not involve a database server.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +github_account = 'akopytov' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['e8ee79b1f399b2d167e6a90de52ccc90e52408f7ade1b9b7135727efe181347f'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('libtool', '2.4.7'), + ('MariaDB', '10.11.2'), + ('PostgreSQL', '15.2'), # optional +] + +preconfigopts = './autogen.sh &&' +configopts = '--with-pgsql ' # optional + +sanity_check_paths = { + 'files': ['bin/sysbench'], + 'dirs': ['bin', 'share'] +} + +sanity_check_commands = ['sysbench --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.3.0.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.3.0.eb new file mode 100644 index 000000000000..99fc626c6820 --- /dev/null +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'TOML-Fortran' +version = '0.3.1' + +homepage = 'https://github.com/toml-f/toml-f' +description = 'TOML parser for Fortran projects' + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7586f0be7dc88dddba4d4e42059b84baa2688a2784bdc1d1f37112ab3edb88e1'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['lib/libtoml-f.a'], + 'dirs': ['include/toml-f', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/TOPAS/TOPAS-3.9-foss-2022b.eb b/easybuild/easyconfigs/t/TOPAS/TOPAS-3.9-foss-2022b.eb new file mode 100644 index 000000000000..294567fbc073 --- /dev/null +++ b/easybuild/easyconfigs/t/TOPAS/TOPAS-3.9-foss-2022b.eb @@ -0,0 +1,54 @@ +easyblock = 'Bundle' + +name = 'TOPAS' +version = '3.9' + +homepage = 'https://www.topasmc.org' +description = """TOPAS wraps and extends the Geant4 Simulation Toolkit to make advanced Monte Carlo simulation of all +forms of radiotherapy easier to use for medical physicists.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('expat', '2.4.9'), + ('X11', '20221110'), + ('Mesa', '22.2.4'), + ('libGLU', '9.0.2'), + ('Qt5', '5.15.7'), + ('HarfBuzz', '5.3.1'), + ('GDCM', '3.0.21'), + ('CLHEP', '2.4.6.4'), +] + +local_geant4_configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +local_geant4_configopts += " -DCLHEP_ROOT_DIR=$EBROOTCLHEP -DGEANT4_INSTALL_DATA=OFF -DGEANT4_BUILD_MULTITHREADED=ON " + +components = [ + # TOPAS required Geant4 10.x, which must be built with multi-threading support + ('Geant4', '10.7.4', { + 'github_account': 'Geant4', + 'source_urls': [GITHUB_SOURCE], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}], + 'checksums': ['602b41dfee1fa6b33b026d00c5bd940155d7e5d0b3495230a87e2a25b28f9996'], + 'start_dir': 'geant4-%(version)s', + 'configopts': local_geant4_configopts, + }), + (name, version, { + 'easyblock': 'CMakeMake', + 'download_instructions': "Manual download required, see https://www.topasmc.org/download", + 'sources': ['topas_%(version_major)s_%(version_minor)s.zip'], + 'checksums': ['57739f8df5fe58f47b2cc5ac646b4776ab137d52640c6e5b1f6cd199ed3c7b0f'], + 'start_dir': 'topas_%(version_major)s_%(version_minor)s', + }), +] + +sanity_check_paths = { + 'files': ['bin/topas', 'lib/libchemistry.a', 'lib/libG4run.%s' % SHLIB_EXT, 'lib/libmain.a', 'lib/libphysics.a'], + 'dirs': ['examples', 'include'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..a85651a4106e --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.13' + +homepage = 'https://www.tcl.tk/' +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['43a1fae7412f61ff11de2cfd05d28cfc3a73762f354a417c62370a54e2caf066'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('zlib', '1.2.13'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..172e63870992 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.13-GCCcore-13.1.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.13' + +homepage = 'https://www.tcl.tk/' +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['43a1fae7412f61ff11de2cfd05d28cfc3a73762f354a417c62370a54e2caf066'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('zlib', '1.2.13'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb index 77b91670e2c4..634b72ba92b9 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b-CUDA-11.4.1.eb @@ -17,7 +17,6 @@ builddependencies = [ ('git', '2.33.1', '-nodocs'), ('pybind11', '2.7.1'), ('UnZip', '6.0'), - ('LLVM', '12.0.1'), # for debugging with llvm-symbolizer, to be removed ] dependencies = [ ('CUDA', '11.4.1', '', SYSTEM), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb index ae6d7df989ce..e2c8fdba601e 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.7.1-foss-2021b.eb @@ -16,7 +16,6 @@ builddependencies = [ ('git', '2.33.1', '-nodocs'), ('pybind11', '2.7.1'), ('UnZip', '6.0'), - ('LLVM', '12.0.1'), # for debugging with llvm-symbolizer, to be removed ] dependencies = [ ('Python', '3.9.6'), diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb index 302f3bd958db..fdeaf3afa245 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb @@ -16,7 +16,6 @@ builddependencies = [ ('git', '2.33.1', '-nodocs'), ('pybind11', '2.7.1'), ('UnZip', '6.0'), - ('LLVM', '12.0.1'), # for debugging with llvm-symbolizer, to be removed ] dependencies = [ ('Python', '3.9.6'), diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..0779ba13c452 --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.10-GCCcore-11.3.0.eb @@ -0,0 +1,46 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# Updated to version 0.6.2: Pavel Grochal (INUITS) +# Updated to version 0.6.5: Alex Domingo (VUB) +# Updated to version 0.6.7 by J. Sassmannshausen NHS/GSTT + +easyblock = 'Tarball' + +name = 'Trim_Galore' +version = '0.6.10' + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """Trim Galore! is a wrapper script to automate quality and adapter +trimming as well as quality control, with some added functionality to remove biased +methylation positions for RRBS sequence files (for directional, non-directional +(or paired-end) sequencing).""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['3a4e414fc658d6eb4356f1572351204e8475a9d7dc79f6798270b57d35bda017'] + +dependencies = [ + ('Python', '3.10.4'), + ('Java', '11', '', SYSTEM), + ('pigz', '2.7'), + ('Perl', '5.34.1'), + ('cutadapt', '4.2'), + ('FastQC', '0.11.9', '-Java-%(javaver)s', SYSTEM), +] + +postinstallcmds = [ + "mkdir %(installdir)s/bin && mv %(installdir)s/%(namelower)s %(installdir)s/bin/%(namelower)s", +] + +fix_perl_shebang_for = ['bin/%(namelower)s'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = [('%(namelower)s', '-v')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb new file mode 100644 index 000000000000..5f9d39b5c69f --- /dev/null +++ b/easybuild/easyconfigs/t/Trimmomatic/Trimmomatic-0.39-Java-17.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'Tarball' + +name = 'Trimmomatic' +version = '0.39' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.usadellab.org/cms/?page=trimmomatic' +description = """Trimmomatic performs a variety of useful trimming tasks for illumina + paired-end and single ended data.The selection of trimming steps and their associated + parameters are supplied on the command line. """ + +toolchain = SYSTEM + +source_urls = ['http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/'] +sources = [SOURCE_ZIP] +checksums = ['2f97e3a237378d55c221abfc38e4b11ea232c8a41d511b8b4871f00c0476abca'] + +dependencies = [('Java', '17')] + +modloadmsg = """To execute Trimmomatic run: java -jar $EBROOTTRIMMOMATIC/trimmomatic-%(version)s.jar\n""" + +sanity_check_paths = { + 'files': ["trimmomatic-%(version)s.jar"], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3-GCC-11.2.0.eb b/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3-GCC-11.2.0.eb new file mode 100755 index 000000000000..4a007546c504 --- /dev/null +++ b/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3-GCC-11.2.0.eb @@ -0,0 +1,43 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'CMakeMake' + +name = 'Triplexator' +version = '1.3.3' + +homepage = "https://github.com/Gurado/triplexator" +description = """Triplexator is a tool for detecting nucleic acid triple helices and triplex features in nucleotide + sequences using the canonical triplex-formation rules.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'Gurado' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['Triplexator-1.3.3_support-modern-compilers.patch'] +checksums = [ + {'v1.3.3.tar.gz': '24b862062ea36bef67beaa9fcade7860450f98c14dcfa499fca666e2b8c570b2'}, + {'Triplexator-1.3.3_support-modern-compilers.patch': + '1c2bee4aab6693c1f5836eb1688a4345b1ff5fa22333bf3252eb749f15995e64'}, +] + +builddependencies = [ + ('CMake', '3.22.1'), +] + +dependencies = [ + ('Boost', '1.79.0'), +] + +# The above patch makes the code buildable with CMAKE_CXX_STANDARD 11, so set that here +configopts = '-DCMAKE_CXX_STANDARD=11' + +sanity_check_commands = [ + "cd %(builddir)s/%(namelower)s-%(version)s && ./demos/smoketest_triplexator.sh %(installdir)s/bin/%(namelower)s" +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3_support-modern-compilers.patch b/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3_support-modern-compilers.patch new file mode 100755 index 000000000000..3a10a3a2639a --- /dev/null +++ b/easybuild/easyconfigs/t/Triplexator/Triplexator-1.3.3_support-modern-compilers.patch @@ -0,0 +1,113 @@ +From e1f86e7df06dd53f0af242858db3909eaa35dac6 Mon Sep 17 00:00:00 2001 +From: amatria +Date: Thu, 8 Sep 2022 12:41:02 +0200 +Subject: [PATCH] compile with a modern c++ compiler + +--- + src/seqan/file/file_format.h | 32 +++++++++---------- + .../parallel/parallel_generated_forwards.h | 2 +- + src/seqan/parallel/parallel_splitting.h | 6 ++-- + src/triplexator.cpp | 4 +-- + 4 files changed, 23 insertions(+), 21 deletions(-) + +diff --git a/src/seqan/file/file_format.h b/src/seqan/file/file_format.h +index da64632..d6df116 100644 +--- a/src/seqan/file/file_format.h ++++ b/src/seqan/file/file_format.h +@@ -205,27 +205,27 @@ struct FileFormat + ~FileFormat() {} + FileFormat const & operator =(FileFormat const &) { return *this; } + +- virtual void * +- formatID_() const = 0; ++ void * ++ formatID_(); + +- virtual void +- read_(TFile & file, TData & data) const = 0; +- virtual void +- read_(TFile & file, TData & data, TSize limit) const = 0; ++ void ++ read_(TFile & file, TData & data); ++ void ++ read_(TFile & file, TData & data, TSize limit); + +- virtual void +- readMeta_(TFile & file, TMeta & meta) const = 0; ++ void ++ readMeta_(TFile & file, TMeta & meta); + +- virtual void +- goNext_(TFile & file) const = 0; ++ void ++ goNext_(TFile & file); + +- virtual TSize +- length_(TFile & file) const = 0; ++ TSize ++ length_(TFile & file); + +- virtual void +- write_(TFile & file, TData & data) const = 0; +- virtual void +- write_(TFile & file, TData & data, TMeta & meta) const = 0; ++ void ++ write_(TFile & file, TData & data); ++ void ++ write_(TFile & file, TData & data, TMeta & meta); + + }; + +diff --git a/src/seqan/parallel/parallel_generated_forwards.h b/src/seqan/parallel/parallel_generated_forwards.h +index 78e9e3e..682bd45 100644 +--- a/src/seqan/parallel/parallel_generated_forwards.h ++++ b/src/seqan/parallel/parallel_generated_forwards.h +@@ -57,7 +57,7 @@ namespace seqan { + //____________________________________________________________________________ + // computeSplitters + +-template void computeSplitters(String & splitters, TSize size, TCount count); // "/Users/fabianbuske/Documents/research/triplex/seqan/core/include/seqan/parallel/parallel_splitting.h"(64) ++template void computeSplitters(TPosString & splitters, TSize size, TCount count); // "/Users/fabianbuske/Documents/research/triplex/seqan/core/include/seqan/parallel/parallel_splitting.h"(64) + + } //namespace seqan + +diff --git a/src/seqan/parallel/parallel_splitting.h b/src/seqan/parallel/parallel_splitting.h +index f8d862f..1ed786d 100755 +--- a/src/seqan/parallel/parallel_splitting.h ++++ b/src/seqan/parallel/parallel_splitting.h +@@ -59,9 +59,11 @@ computeSplitters(splitters, 10, 5); + ..include:seqan/parallel.h + */ + +-template +-void computeSplitters(String & splitters, TSize size, TCount count) ++template ++void computeSplitters(TPosString & splitters, TSize size, TCount count) + { ++ typedef typename Value::Type TPos; ++ + resize(splitters, count + 1); + splitters[0] = 0; + TSize blockLength = size / count; +diff --git a/src/triplexator.cpp b/src/triplexator.cpp +index a3738cb..d6d8e7f 100644 +--- a/src/triplexator.cpp ++++ b/src/triplexator.cpp +@@ -917,7 +917,7 @@ namespace SEQAN_NAMESPACE_MAIN + appendValue(duplexNames, id, Generous()); + + read(file, duplexString, Fasta()); // read Fasta sequence +- ttsnoToFileMap.insert(::std::make_pair >(seqNo,::std::make_pair< ::std::string,unsigned>(filename,seqNoWithinFile))); ++ ttsnoToFileMap.insert(::std::make_pair >(::std::move(seqNo),::std::make_pair< ::std::string,unsigned>(::std::move(filename),::std::move(seqNoWithinFile)))); + + if (options._debugLevel > 1 ) + options.logFileHandle << _getTimeStamp() << " ... Finished reading next duplex sequence" << ::std::endl; +@@ -1040,7 +1040,7 @@ namespace SEQAN_NAMESPACE_MAIN + readShortID(file, id, Fasta()); // read Fasta id up to first whitespace + appendValue(duplexNames, id, Generous()); + read(file, duplexString, Fasta()); // read Fasta sequence +- ttsnoToFileMap.insert(::std::make_pair >(seqNo,::std::make_pair< ::std::string,unsigned>(filename,seqNoWithinFile))); ++ ttsnoToFileMap.insert(::std::make_pair >(::std::move(seqNo),::std::make_pair< ::std::string,unsigned>(::std::move(filename),::std::move(seqNoWithinFile)))); + appendValue(duplexSet, duplexString); + + if (options._debugLevel > 1 ) diff --git a/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-GCC-11.2.0.eb b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-GCC-11.2.0.eb new file mode 100644 index 000000000000..8260f1d0d1fe --- /dev/null +++ b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-GCC-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'tRNAscan-SE' +version = '2.0.12' + +homepage = 'https://github.com/UCSC-LoweLab/tRNAscan-SE' +description = "A program for detection of tRNA genes" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/UCSC-LoweLab/tRNAscan-SE/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4b255c2c5e0255381194166f857ab2ea21c55aa7de409e201333ba615aa3dc61'] + +dependencies = [ + ('Perl', '5.34.0'), +] + +fix_perl_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/covels-SE', 'bin/tRNAscan-SE'], + 'dirs': ['include', 'lib/tRNAscan-SE'], +} + +sanity_check_commands = ["tRNAscan-SE --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2022b.eb b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2022b.eb new file mode 100644 index 000000000000..f65eb9761f86 --- /dev/null +++ b/easybuild/easyconfigs/t/tRNAscan-SE/tRNAscan-SE-2.0.12-foss-2022b.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'tRNAscan-SE' +version = '2.0.12' + +homepage = 'http://trna.ucsc.edu/tRNAscan-SE/' +description = """tRNAscan-SE is the most widely employed tool for identifying + and annotating tRNA genes in genomes.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['http://trna.ucsc.edu/software/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['96fa4af507cd918c1c623763d9260bd6ed055d091662b44314426f6bbf447251'] + +dependencies = [ + ('Autoconf', '2.69', '', SYSTEM), + ('Infernal', '1.1.4'), +] + +sanity_check_paths = { + 'files': [ + 'bin/tRNAscan-SE', + 'lib/tRNAscan-SE/tRNAscanSE/tRNA.pm', + ], + 'dirs': [ + 'bin', + 'include', + 'lib', + ], +} + +# tRNAscan-SE.conf sets the Infernal bin directory to be ours. +postinstallcmds = [ + "for b in $(ls $EBROOTINFERNAL/bin); do ln -s $EBROOTINFERNAL/bin/$b %(installdir)s/bin; done", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tantan/tantan-40-GCC-11.2.0.eb b/easybuild/easyconfigs/t/tantan/tantan-40-GCC-11.2.0.eb new file mode 100644 index 000000000000..b6064225cd3c --- /dev/null +++ b/easybuild/easyconfigs/t/tantan/tantan-40-GCC-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'tantan' +version = '40' + +homepage = 'https://gitlab.com/mcfrith/tantan' +description = "tantan identifies simple regions / low complexity / tandem repeats in DNA or protein sequences" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://gitlab.com/mcfrith/tantan/-/archive/%(version)s/'] +sources = ['tantan-%(version)s.tar.gz'] +checksums = ['61303c88cdf41fa5bcb5f77f674b4fac2a9bc0e4c9abb3b9d75af35c47162240'] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/tantan'], + 'dirs': [], +} + +sanity_check_commands = ["tantan --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.24.07-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.07-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..f2a441e8129b --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.07-GCCcore-12.2.0.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.24.07' + +homepage = 'https://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [ + 'https://astron.com/pub/%(namelower)s', + 'https://astron.com/pub/%(namelower)s/old', + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['74e4e9805cbd9413ed34b4ffa1d72fc8d0ef81a5b79476854091416ce9336995'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('ncurses', '6.3')] + +postinstallcmds = ["ln -s tcsh %(installdir)s/bin/csh"] + +sanity_check_paths = { + 'files': ["bin/tcsh", "bin/csh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb index fed7c2635a0f..9bf893a4d12f 100644 --- a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb @@ -43,7 +43,7 @@ dependencies = [ ('Pango', '1.50.7'), ] -separate_build_dir = True +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] postinstallcmds = [ 'rm %(builddir)s/tessdata_best-4.1.0/configs', @@ -56,7 +56,7 @@ modextrapaths = { } sanity_check_paths = { - 'files': ['bin/tesseract'], + 'files': ['bin/tesseract', 'lib/libtesseract.a', 'lib/libtesseract.%s' % SHLIB_EXT], 'dirs': ['share/tessdata', 'include/tesseract'] } diff --git a/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb index 7c74e626642c..27046de748bb 100644 --- a/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/t/texlive/texlive-20200406-GCCcore-8.3.0.eb @@ -4,6 +4,7 @@ easyblock = 'Tarball' name = 'texlive' version = '20200406' +local_version_year = version[:4] homepage = 'https://tug.org' description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript @@ -13,7 +14,10 @@ description = """TeX is a typesetting language. Instead of visually formatting y toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = ['ftp://tug.org/texlive/historic/2020/'] +source_urls = [ + 'ftp://tug.org/texlive/historic/%s/' % local_version_year, + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_version_year, +] sources = [ { 'download_filename': 'install-tl-unx.tar.gz', @@ -41,10 +45,11 @@ postinstallcmds = [ 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' + ' -repository ' + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_version_year ] modextrapaths = { - 'PATH': 'bin/x86_64-linux', + 'PATH': 'bin/%(arch)s-linux', 'INFOPATH': 'texmf-dist/doc/info', 'MANPATH': 'texmf-dist/doc/man', } @@ -53,8 +58,8 @@ modextravars = { } sanity_check_paths = { - 'files': ['bin/x86_64-linux/tex', 'bin/x86_64-linux/latex'], - 'dirs': ['bin/x86_64-linux', 'texmf-dist'], + 'files': ['bin/%(arch)s-linux/tex', 'bin/%(arch)s-linux/latex'], + 'dirs': ['bin/%(arch)s-linux', 'texmf-dist'], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb index 9809666eaa4f..97dde3d44ad6 100644 --- a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-10.3.0.eb @@ -4,6 +4,7 @@ easyblock = 'Tarball' name = 'texlive' version = '20210324' +local_version_year = version[:4] homepage = 'https://tug.org' description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript @@ -14,8 +15,8 @@ description = """TeX is a typesetting language. Instead of visually formatting y toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = [ - 'ftp://tug.org/texlive/historic/2021/', - 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2021/', + 'ftp://tug.org/texlive/historic/%s/' % local_version_year, + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_version_year, ] sources = [ { @@ -44,6 +45,7 @@ postinstallcmds = [ 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' + ' -repository ' + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_version_year ] modextrapaths = { diff --git a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb index b00d0026d53b..dc4af0f23aeb 100644 --- a/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/t/texlive/texlive-20210324-GCC-11.2.0.eb @@ -4,6 +4,7 @@ easyblock = 'Tarball' name = 'texlive' version = '20210324' +local_version_year = version[:4] homepage = 'https://tug.org' description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript @@ -14,8 +15,8 @@ description = """TeX is a typesetting language. Instead of visually formatting y toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = [ - 'ftp://tug.org/texlive/historic/2021/', - 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2021/', + 'ftp://tug.org/texlive/historic/%s/' % local_version_year, + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_version_year, ] sources = [ { @@ -44,6 +45,7 @@ postinstallcmds = [ 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' + ' -repository ' + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_version_year ] modextrapaths = { diff --git a/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb index d249ac772bfa..464451489225 100644 --- a/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/t/texlive/texlive-20220321-GCC-11.2.0.eb @@ -4,6 +4,7 @@ easyblock = 'Tarball' name = 'texlive' version = '20220321' +local_version_year = version[:4] homepage = 'https://tug.org' description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript @@ -14,8 +15,8 @@ description = """TeX is a typesetting language. Instead of visually formatting y toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = [ - 'ftp://tug.org/texlive/historic/2022/', - 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/2022/', + 'ftp://tug.org/texlive/historic/%s/' % local_version_year, + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_version_year, ] sources = [ { @@ -44,6 +45,7 @@ postinstallcmds = [ 'echo "TEXMFSYSCONFIG %(installdir)s/texmf-config" >> %(installdir)s/texlive.profile && ' 'echo "TEXMFSYSVAR %(installdir)s/texmf-var" >> %(installdir)s/texlive.profile && ' '%(builddir)s/install-tl-%(version)s/install-tl -profile %(installdir)s/texlive.profile' + ' -repository ' + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_version_year ] modextrapaths = { diff --git a/easybuild/easyconfigs/t/thirdorder/thirdorder-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/t/thirdorder/thirdorder-1.1.1-foss-2022a.eb new file mode 100644 index 000000000000..9ef61b93414b --- /dev/null +++ b/easybuild/easyconfigs/t/thirdorder/thirdorder-1.1.1-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' +name = 'thirdorder' +version = '1.1.1' + +homepage = 'https://bitbucket.org/sousaw/thirdorder/' +description = """A Python script to help create input files for computing anhamonic +interatomic force constants, harnessing the symmetries of the system to minimize the +number of required DFT calculations. A second mode of operation allows the user to +build the third-order IFC matrix from the results of those runs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('spglib', '2.0.2'), +] + +source_urls = ['https://bitbucket.org/sousaw/thirdorder/get/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f95e6371d78231d68028ec4e28d1d45ce60b1093e64f87e4b0cdb259375cd0d4'] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# Thirdorder need to be built using Cython and it needs to have a version in setup.py +preinstallopts = r'sed -i -e "s/^USE_CYTHON.*/USE_CYTHON=True/" ' +preinstallopts += r'-e "s/^\(setup(.*\))$/\1, version=\"%(version)s\")/" setup.py && ' + +options = {'modulename': 'thirdorder_core'} + +postinstallcmds = ["mkdir %(installdir)s/bin && cp thirdorder_*.py %(installdir)s/bin/"] + +sanity_check_paths = { + 'files': ['bin/thirdorder_%s.py' % x for x in ["castep", "espresso", "vasp"]], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..e241a9de1bce --- /dev/null +++ b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'time' +version = '1.9' + +homepage = 'https://www.gnu.org/software/time/' +description = """The `time' command runs another program, then displays information about the resources used by that + program, collected by the system while the program was running.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['fbacf0c81e62429df3e33bda4cee38756604f18e01d977338e23306a3e3b521e'] + +builddependencies = [('binutils', '2.39')] + +postinstallcmds = ["ln -s %(installdir)s/bin/%(name)s %(installdir)s/bin/gtime"] + +sanity_check_paths = { + 'files': ['bin/gtime', 'bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["time echo test"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb new file mode 100644 index 000000000000..4a6496524393 --- /dev/null +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1-foss-2022a-PyTorch-1.12.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonPackage' + +name = 'torchtext' +version = '0.14.1' +local_pytorch_version = '1.12.0' +versionsuffix = '-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/text' +description = "Data loaders and abstractions for text and NLP" + +toolchain = {'name': 'foss', 'version': '2022a'} + +# Sources are no longer available in PyPI, it only has wheels +source_urls = ['https://github.com/pytorch/text/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['torchtext-0.14.1_deps_fix.patch'] +checksums = [ + {'v0.14.1.tar.gz': 'fd1ef3da7d9c20408c740f7dc7d02ad52a6048b46368355a1a7326d3bc4f2e63'}, + {'torchtext-0.14.1_deps_fix.patch': '3830747bfb3624a94efa8c8132b1764277b38f3b80cc9f452fba2475465d7ec1'}, +] + +builddependencies = [ + ('RE2', '2022-06-01'), + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('SentencePiece', '0.1.97'), + ('tqdm', '4.64.0'), + ('PyTorch', local_pytorch_version), + ('double-conversion', '3.2.0'), + ('utf8proc', '2.7.0'), +] + +download_dep_fail = True, +use_pip = True +sanity_pip_check = True, + +# Disable bundled libraries to use those from EB: RE2, SentencePiece +preinstallopts = "sed -i '/third_party/d;/^_init_submodule/d' setup.py && " + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch new file mode 100644 index 000000000000..1212651426e4 --- /dev/null +++ b/easybuild/easyconfigs/t/torchtext/torchtext-0.14.1_deps_fix.patch @@ -0,0 +1,54 @@ +The error "string_view has not been declared in std" appears when not using C++17 +diff -u text/CMakeLists.txt.orig text/CMakeLists.txt +--- text/CMakeLists.txt.orig 2023-03-08 14:33:35.618931003 +0100 ++++ text/CMakeLists.txt 2023-03-08 14:35:03.169072623 +0100 +@@ -24,10 +24,10 @@ + if(env_cxx_standard GREATER -1) + message( + WARNING "C++ standard version definition detected in environment variable." +- "PyTorch requires -std=c++14. Please remove -std=c++ settings in your environment.") ++ "PyTorch requires -std=c++17. Please remove -std=c++ settings in your environment.") + endif() + +-set(CMAKE_CXX_STANDARD 14) ++set(CMAKE_CXX_STANDARD 17) + set(CMAKE_C_STANDARD 11) + + set(CMAKE_EXPORT_COMPILE_COMMANDS ON) +@@ -63,5 +63,10 @@ + + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_COMPILED_WITH_CXX_ABI} -Wall ${TORCH_CXX_FLAGS}") + +-add_subdirectory(third_party) ++find_package(double-conversion) ++find_package(re2) ++find_library(SENTENCEPIECE_LIBRARY sentencepiece PATHS $ENV{EBROOTSENTENCEPIECE}/lib64) ++find_library(SENTENCEPIECE_TRAIN_LIBRARY sentencepiece_train PATHS $ENV{EBROOTSENTENCEPIECE}/lib64) ++find_library(UTF8PROC_LIBRARY utf8proc PATHS $ENV{UTF8PROC}/lib64) ++ + add_subdirectory(torchtext/csrc) +diff -u text/torchtext/csrc/CMakeLists.txt.orig text/torchtext/csrc/CMakeLists.txt +--- text/torchtext/csrc/CMakeLists.txt.orig 2023-03-08 14:11:53.387582628 +0100 ++++ text/torchtext/csrc/CMakeLists.txt 2023-03-08 14:16:11.159140070 +0100 +@@ -18,10 +18,6 @@ + set( + LIBTORCHTEXT_INCLUDE_DIRS + ${PROJECT_SOURCE_DIR} +- ${PROJECT_SOURCE_DIR}/third_party/sentencepiece/src +- $ +- $ +- $ + ${TORCH_INSTALL_PREFIX}/include + ${TORCH_INSTALL_PREFIX}/include/torch/csrc/api/include + ) +@@ -119,10 +115,6 @@ + set( + EXTENSION_INCLUDE_DIRS + ${PROJECT_SOURCE_DIR} +- ${PROJECT_SOURCE_DIR}/third_party/sentencepiece/src +- $ +- $ +- $ + ${TORCH_INSTALL_PREFIX}/include + ${TORCH_INSTALL_PREFIX}/include/torch/csrc/api/include + ) diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..3391b0d006e9 --- /dev/null +++ b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.2.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated by: +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'MakeCp' + +name = 'trimAl' +version = '1.4.1' + +homepage = 'https://github.com/scapella/trimal' +description = """EVB, FEP and LIE simulator.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'scapella' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e'] + +builddependencies = [ + ('binutils', '2.37'), + +] +start_dir = 'source' + +files_to_copy = [(['trimal', 'readal', 'statal'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/trimal', 'bin/readal', 'bin/statal'], + 'dirs': [] +} + +sanity_check_commands = ["trimal -h"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..8da2ca94e6c9 --- /dev/null +++ b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated by: +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'MakeCp' + +name = 'trimAl' +version = '1.4.1' + +homepage = 'https://github.com/scapella/trimal' +description = """EVB, FEP and LIE simulator.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'scapella' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e'] + +builddependencies = [ + ('binutils', '2.38'), + +] +start_dir = 'source' + +files_to_copy = [(['trimal', 'readal', 'statal'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/trimal', 'bin/readal', 'bin/statal'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/trimesh/trimesh-3.21.5-gfbf-2022b.eb b/easybuild/easyconfigs/t/trimesh/trimesh-3.21.5-gfbf-2022b.eb new file mode 100644 index 000000000000..b0321430d599 --- /dev/null +++ b/easybuild/easyconfigs/t/trimesh/trimesh-3.21.5-gfbf-2022b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'trimesh' +version = '3.21.5' + +homepage = 'https://trimsh.org/' +description = """Trimesh is a Python (2.7- 3.3+) library for loading and using triangular meshes with an emphasis on +watertight meshes. The goal of the library is to provide a fully featured Trimesh object which allows for easy +manipulation and analysis, in the style of the excellent Polygon object in the Shapely library.""" + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['74741bc7f9fcb94b98951db8dc8ec8364a2ef52ac2ca0761c7ba06182ef329be'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), # numpy required +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb b/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb new file mode 100644 index 000000000000..0fa522cb25d6 --- /dev/null +++ b/easybuild/easyconfigs/t/turbinesFoam/turbinesFoam-20220516-foss-2020a-OpenFOAM-8.eb @@ -0,0 +1,35 @@ +easyblock = 'CmdCp' + +name = 'turbinesFoam' +version = '20220516' +_openfoamver = '8' +_commit = '480eeef' +versionsuffix = '-OpenFOAM-%s' % _openfoamver + +homepage = 'https://github.com/turbinesFoam/turbinesFoam' +description = """ +turbinesFoam is a library for simulating wind and marine hydrokinetic turbines +in OpenFOAM using the actuator line method. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +github_account = 'turbinesFoam' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['2e13faec8b2489e91108ea3fc8eb31b1b32bb1478e608853c9cfa9b78a3206d1'] + +dependencies = [ + ('OpenFOAM', _openfoamver), +] + +cmds_map = [('.*', 'source "$FOAM_BASH" && FOAM_USER_LIBBIN="$PWD/lib" ./Allwmake')] + +files_to_copy = ['lib'] + +sanity_check_paths = { + 'files': ['lib/libturbinesFoam.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb new file mode 100644 index 000000000000..bfe211063d3b --- /dev/null +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -0,0 +1,57 @@ +easyblock = 'ConfigureMake' + +name = 'UCC-CUDA' +version = '1.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.openucx.org/' +description = """UCC (Unified Collective Communication) is a collective +communication operations API and library that is flexible, complete, and +feature-rich for current and emerging programming models and runtimes. + +This module adds the UCC CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-1.0.0_link_against_existing_UCC_libs.patch', + '%(name)s-%(version)s_cuda_12_mem_ops.patch', +] +checksums = [ + {'v1.1.0.tar.gz': '74c8ba75037b5bd88cb703e8c8ae55639af3fecfd4428912a433c010c97b4df7'}, + {'UCC-CUDA-1.0.0_link_against_existing_UCC_libs.patch': + '9fa11cf6779174f4e9048df5812096e4261e1769d465cc7f34a6354398876856'}, + {'UCC-CUDA-1.1.0_cuda_12_mem_ops.patch': 'fc3ea1487d29dc626db2363ef5a79e7f0906f6a7507a363fa6167a812b143eb6'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('UCC', '1.1.0'), + ('CUDA', '12.0.0', '', SYSTEM), + ('UCX-CUDA', '1.13.1', '-CUDA-%(cudaver)s'), + ('NCCL', '2.16.2', '-CUDA-%(cudaver)s'), +] + +preconfigopts = "./autogen.sh && " + +buildopts = '-C src/components/mc/cuda V=1 && make -C src/components/tl/nccl V=1' +installopts = '-C src/components/mc/cuda && make -C src/components/tl/nccl install' + +sanity_check_paths = { + 'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +modextrapaths = {'EB_UCC_EXTRA_COMPONENT_PATH': 'lib/ucc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0_cuda_12_mem_ops.patch b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0_cuda_12_mem_ops.patch new file mode 100644 index 000000000000..36212b970db1 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.1.0_cuda_12_mem_ops.patch @@ -0,0 +1,99 @@ +Backported fix for CUDA 12 https://github.com/openucx/ucc/pull/700 +Essentially just removes the deprecated checks for CUDA MEM OPS as they are required in CUDA 12 +author: micketeer@gmail.com +--- src/components/ec/cuda/ec_cuda.c.orig 2023-02-02 18:44:36.085221084 +0000 ++++ src/components/ec/cuda/ec_cuda.c 2023-02-02 18:47:23.726819030 +0000 +@@ -205,11 +205,10 @@ + { + ucc_ec_cuda_config_t *cfg = EC_CUDA_CONFIG; + ucc_status_t status; +- int device, num_devices, attr; ++ int device, num_devices; + CUdevice cu_dev; + CUresult cu_st; + cudaError_t cuda_st; +- const char *cu_err_st_str; + + ucc_ec_cuda.stream = NULL; + ucc_ec_cuda.stream_initialized = 0; +@@ -272,9 +271,14 @@ + } else { + ucc_ec_cuda.strm_task_mode = UCC_EC_CUDA_TASK_MEM_OPS; + ucc_ec_cuda.post_strm_task = ucc_ec_cuda_post_driver_stream_task; ++#if CUDA_VERSION < 12000 ++ CUresult cu_st; ++ CUdevice cu_dev; ++ int attr; + + cu_st = cuCtxGetDevice(&cu_dev); + if (cu_st != CUDA_SUCCESS){ ++ const char *cu_err_st_str; + cuGetErrorString(cu_st, &cu_err_st_str); + ec_debug(&ucc_ec_cuda.super, "cuCtxGetDevice() failed: %s", + cu_err_st_str); +@@ -297,6 +301,7 @@ + "CUDA MEM OPS are not supported or disabled"); + return UCC_ERR_NOT_SUPPORTED; + } ++#endif + } + ucc_ec_cuda.task_strm_type = cfg->task_strm_type; + ucc_spinlock_init(&ucc_ec_cuda.init_spinlock, 0); +--- src/components/tl/nccl/tl_nccl_context.c.orig 2023-02-03 15:17:09.358881676 +0000 ++++ src/components/tl/nccl/tl_nccl_context.c 2023-02-03 17:04:31.680185749 +0000 +@@ -101,13 +101,14 @@ + ucc_derived_of(config, ucc_tl_nccl_context_config_t); + int mem_ops_attr = 0; + ucc_status_t status; +- CUresult cu_st; +- CUdevice cu_dev; + + UCC_CLASS_CALL_SUPER_INIT(ucc_tl_context_t, &tl_nccl_config->super, + params->context); + memcpy(&self->cfg, tl_nccl_config, sizeof(*tl_nccl_config)); + if (self->cfg.sync_type != UCC_TL_NCCL_COMPLETION_SYNC_TYPE_EVENT) { ++#if CUDA_VERSION < 12000 ++ CUresult cu_st; ++ CUdevice cu_dev; + cu_st = cuCtxGetDevice(&cu_dev); + if (cu_st == CUDA_SUCCESS) { + cu_st = cuDeviceGetAttribute(&mem_ops_attr, +@@ -116,6 +117,9 @@ + } else { + tl_info(self->super.super.lib, "failed to get cuda device"); + } ++#else ++ mem_ops_attr = 1; ++#endif + if (mem_ops_attr == 0) { + if (self->cfg.sync_type == UCC_TL_NCCL_COMPLETION_SYNC_TYPE_MEMOPS) { + tl_error(self->super.super.lib, "memops not supported"); +--- config/m4/cuda.m4.orig 2023-02-03 17:04:44.367155175 +0000 ++++ config/m4/cuda.m4 2023-02-03 17:06:26.110909987 +0000 +@@ -15,6 +15,11 @@ + ARCH10="-gencode=arch=compute_75,code=sm_75" + ARCH11="-gencode=arch=compute_80,code=sm_80 \ + -gencode=arch=compute_80,code=compute_80" ++ARCH111="-gencode=arch=compute_86,code=sm_86 \ ++-gencode=arch=compute_86,code=compute_86" ++ARCH120="-gencode=arch=compute_90,code=sm_90 \ ++-gencode=arch=compute_90,code=compute_90" ++ + + AC_DEFUN([CHECK_CUDA],[ + AS_IF([test "x$cuda_checked" != "xyes"], +@@ -104,8 +109,12 @@ + [NVCC_CFLAGS="$NVCC_CFLAGS -O3 -g -DNDEBUG"]) + AS_IF([test "x$cuda_happy" = "xyes"], + [AS_IF([test "x$with_nvcc_gencode" = "xdefault"], +- [AS_IF([test $CUDA_MAJOR_VERSION -eq 11], +- [NVCC_ARCH="${ARCH8} ${ARCH9} ${ARCH10} ${ARCH11}"])], ++ [AS_IF([test $CUDA_MAJOR_VERSION -eq 12], ++ [NVCC_ARCH="${ARCH7} ${ARCH8} ${ARCH9} ${ARCH10} ${ARCH110} ${ARCH111} ${ARCH120}"], ++ [AS_IF([test $CUDA_MAJOR_VERSION -eq 11], ++ [AS_IF([test $CUDA_MINOR_VERSION -lt 1], ++ [NVCC_ARCH="${ARCH7} ${ARCH8} ${ARCH9} ${ARCH10} ${ARCH110}"], ++ [NVCC_ARCH="${ARCH7} ${ARCH8} ${ARCH9} ${ARCH10} ${ARCH110} ${ARCH111}"])])])], + [NVCC_ARCH="$with_nvcc_gencode"]) + AC_SUBST([NVCC_ARCH], ["$NVCC_ARCH"])]) + LDFLAGS="$save_LDFLAGS" diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb index b5ff6ef4e426..8c350bb641b0 100644 --- a/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb @@ -14,7 +14,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] -checksums = ['74c8ba75037b5bd88cb703e8c8ae55639af3fecfd4428912a433c010c97b4df7'] +patches = ['UCC-%(version)s-multiple_component_paths.patch'] +checksums = [ + {'v1.1.0.tar.gz': '74c8ba75037b5bd88cb703e8c8ae55639af3fecfd4428912a433c010c97b4df7'}, + {'UCC-1.1.0-multiple_component_paths.patch': '3081d0f694331daa4a88a0fa3fb54b9a918015248ae5eb7b3157b924abd31bee'}, +] builddependencies = [ ('binutils', '2.39'), diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.1.0-multiple_component_paths.patch b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-multiple_component_paths.patch new file mode 100644 index 000000000000..0e13578b55fe --- /dev/null +++ b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-multiple_component_paths.patch @@ -0,0 +1,46 @@ +Adds support for multiple extra components paths to UCC +Was necessary to add, as they broke the logic we used for UCC_COMPONEN_PATH in 1.1.0, +then removed it completely in 1.2.0. +This patch also removes the need to copy over all the other plugins, thus supporting multiple external components. + +author: micketeer@gmail.com + +diff -ru ucc-1.1.0.orig/src/utils/ucc_component.c ucc-1.1.0.fixed/src/utils/ucc_component.c +--- ucc-1.1.0.orig/src/utils/ucc_component.c 2023-04-06 15:16:18.341729973 +0200 ++++ ucc-1.1.0.fixed/src/utils/ucc_component.c 2023-04-08 13:42:28.448319486 +0200 +@@ -128,6 +128,27 @@ + return UCC_ERR_INVALID_PARAM; + } + ++ char *extra_component_path = getenv("EB_UCC_EXTRA_COMPONENT_PATH"); ++ if (extra_component_path) { ++ // Add extra room for extra paths, braces and comma (+3): ++ pattern_size = ++ strlen(ucc_global_config.component_path) + strlen(framework_name) + 16 + strlen(extra_component_path) + 3; ++ full_pattern = (char *)ucc_malloc(pattern_size, "full_pattern"); ++ if (!full_pattern) { ++ ucc_error("failed to allocate %zd bytes for full_pattern", ++ pattern_size); ++ return UCC_ERR_NO_MEMORY; ++ } ++ ucc_snprintf_safe(full_pattern, pattern_size, "{%s,%s}/libucc_%s_*.so", ++ extra_component_path, ucc_global_config.component_path, framework_name); ++ // Replace ; typically used in PATHs variables with , for glob ++ char *current_pos = strchr(full_pattern, ';'); ++ while (current_pos) { ++ *current_pos = ','; ++ current_pos = strchr(current_pos, ';'); ++ } ++ glob(full_pattern, GLOB_BRACE, NULL, &globbuf); ++ } else { + pattern_size = + strlen(ucc_global_config.component_path) + strlen(framework_name) + 16; + full_pattern = (char *)ucc_malloc(pattern_size, "full_pattern"); +@@ -139,6 +160,7 @@ + ucc_snprintf_safe(full_pattern, pattern_size, "%s/libucc_%s_*.so", + ucc_global_config.component_path, framework_name); + glob(full_pattern, 0, NULL, &globbuf); ++ } + ucc_free(full_pattern); + n_loaded = 0; + diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.5.2.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.5.2.eb new file mode 100644 index 000000000000..3748b1ba66a6 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.5.2.eb @@ -0,0 +1,42 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.11.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] +patches = [ + '%(name)s-1.11.0_link_against_existing_UCX_libs.patch', +] +checksums = [ + {'ucx-1.11.2.tar.gz': 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, +] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('UCX', version), + ('CUDA', '11.5.2', '', SYSTEM), + ('GDRCopy', '2.3'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..c84b1e487912 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.14.0-GCCcore-12.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.14.0' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [ + 'UCX-1.13.1-dynamic_modules.patch', +] +checksums = [ + {'ucx-1.14.0.tar.gz': '9bd95e2059de5dece9dddd049aacfca3d21bfca025748a6a0b1be4486e28afdd'}, + {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.3'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.12'), + ('numactl', '2.0.16'), +] + +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --without-go --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..67b179fd4796 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.28' + +homepage = 'https://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/%(version)s/', + 'https://sources.easybuild.io/u/UDUNITS/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['590baec83161a3fd62c00efa66f6113cec8a7c461e3f61a5182167e0cc5d579e'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('expat', '2.5.0')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..7baea9a00a2d --- /dev/null +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.3.0.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'UnZip' +version = '6.0' + +homepage = 'http://www.info-zip.org/UnZip.html' +description = """UnZip is an extraction utility for archives compressed +in .zip format (also called "zipfiles"). Although highly compatible both +with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's +own Zip program, our primary objectives have been portability and +non-MSDOS functionality.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +patches = [ + 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', +] +checksums = [ + '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz + # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch + '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', +] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +local_cf = ['$CFLAGS', '$CPPFLAGS', '-I.', '-DACORN_FTYPE_NFS', '-DWILD_STOP_AT_DIR', '-DLARGE_FILE_SUPPORT' + '-DUNICODE_SUPPORT', '-DUNICODE_WCHAR', '-DUTF8_MAYBE_NATIVE', '-DNO_LCHMOD', '-DDATE_FORMAT=DF_YMD', + '-DUSE_BZIP2', '-DIZ_HAVE_UXUIDGID', '-DNOMEMCPY', '-DNO_WORKING_ISPRINT'] + +buildopts = ' '.join([ + "-f unix/Makefile", + 'CC="$CC"', + 'D_USE_BZ2=-DUSE_BZIP2', + 'L_BZ2=-lbz2', + 'LF2="$LDFLAGS"', + 'CF="%s"' % ' '.join(local_cf), + 'unzips', +]) + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/unzip', 'bin/zipinfo'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["unzip -v"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.1.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..bfb9b30c73c8 --- /dev/null +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-13.1.0.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'UnZip' +version = '6.0' + +homepage = 'http://www.info-zip.org/UnZip.html' +description = """UnZip is an extraction utility for archives compressed +in .zip format (also called "zipfiles"). Although highly compatible both +with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's +own Zip program, our primary objectives have been portability and +non-MSDOS functionality.""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +patches = [ + 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', +] +checksums = [ + '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz + # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch + '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', +] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +local_cf = ['$CFLAGS', '$CPPFLAGS', '-I.', '-DACORN_FTYPE_NFS', '-DWILD_STOP_AT_DIR', '-DLARGE_FILE_SUPPORT' + '-DUNICODE_SUPPORT', '-DUNICODE_WCHAR', '-DUTF8_MAYBE_NATIVE', '-DNO_LCHMOD', '-DDATE_FORMAT=DF_YMD', + '-DUSE_BZIP2', '-DIZ_HAVE_UXUIDGID', '-DNOMEMCPY', '-DNO_WORKING_ISPRINT'] + +buildopts = ' '.join([ + "-f unix/Makefile", + 'CC="$CC"', + 'D_USE_BZ2=-DUSE_BZIP2', + 'L_BZ2=-lbz2', + 'LF2="$LDFLAGS"', + 'CF="%s"' % ' '.join(local_cf), + 'unzips', +]) + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/unzip', 'bin/zipinfo'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["unzip -v"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-11.eb b/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-11.eb new file mode 100644 index 000000000000..920e80869a6f --- /dev/null +++ b/easybuild/easyconfigs/u/unicore-uftp/unicore-uftp-1.4.2-Java-11.eb @@ -0,0 +1,27 @@ +easyblock = 'PackedBinary' + +name = 'unicore-uftp' +version = '1.4.2' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://sourceforge.net/projects/unicore/' +description = """UNICORE Java-based client for UFTP""" + +toolchain = SYSTEM + +source_urls = ['https://downloads.sourceforge.net/project/unicore/Clients/UFTP-Client/%(version)s'] +sources = ['uftp-client-%(version)s-all.zip'] +checksums = ['49670714416077274a0dfdc261e5552bcabbdd5cc4454181a794158491524c54'] + +dependencies = [('Java', '11', '', SYSTEM)] + +postinstallcmds = ["chmod +x %(installdir)s/bin/uftp"] + +sanity_check_paths = { + 'files': ['bin/uftp'], + 'dirs': ['bin', 'lib'], +} + +sanity_check_commands = [('uftp', '-version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..33d5c5ec66ab --- /dev/null +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'utf8proc' +version = '2.8.0' + +homepage = 'https://github.com/JuliaStrings/utf8proc' +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +and other operations for data in the UTF-8 encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a0a60a79fe6f6d54e7d411facbfcc867a6e198608f2cd992490e46f04b1bcecc'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +separate_build_dir = True + +configopts = ['', '-DBUILD_SHARED_LIBS=true'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..74f889da9332 --- /dev/null +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.8.0-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'utf8proc' +version = '2.8.0' + +homepage = 'https://github.com/JuliaStrings/utf8proc' +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +and other operations for data in the UTF-8 encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a0a60a79fe6f6d54e7d411facbfcc867a6e198608f2cd992490e46f04b1bcecc'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +separate_build_dir = True + +configopts = ['', '-DBUILD_SHARED_LIBS=true'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.2.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.2.0.eb new file mode 100644 index 000000000000..0ff539325ea2 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.16' + +homepage = "https://vcftools.github.io" +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3'] + +builddependencies = [ + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('Perl', '5.36.0'), + ('HTSlib', '1.17'), + ('zlib', '1.2.12'), +] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(namelower)s', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Vim/Vim-9.0.1434-GCCcore-12.2.0.eb b/easybuild/easyconfigs/v/Vim/Vim-9.0.1434-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..3ba63172bd88 --- /dev/null +++ b/easybuild/easyconfigs/v/Vim/Vim-9.0.1434-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'Vim' +version = '9.0.1434' + +homepage = 'http://www.vim.org' +description = """ Vim is an advanced text editor that seeks to provide the power + of the de-facto Unix editor 'Vi', with a more complete feature set. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/vim/vim/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f7a43d6f2c08c4d76c5ceb9ab6603fe2d87d56c1162934525cf46362ef8a4e65'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('Perl', '5.36.0'), + ('PCRE', '8.45') +] + +configopts = '--with-features=huge --enable-python3interp=yes --enable-perlinterp=yes' + +sanity_check_paths = { + 'files': ['bin/vim', 'bin/vimtutor', 'bin/xxd'], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = ['vim --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb b/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb new file mode 100644 index 000000000000..e06d4354bf00 --- /dev/null +++ b/easybuild/easyconfigs/v/vispr/vispr-0.4.14-foss-2022a.eb @@ -0,0 +1,47 @@ +# Author: Denis Kristak (Inuits) + +easyblock = 'PythonPackage' + +name = 'vispr' +version = '0.4.14' + +homepage = 'https://pypi.org/project/vispr/' + +description = """ +VISPR - A visualization framework for CRISPR data. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = ['%(name)s-%(version)s.tar.gz'] +patches = [ + 'vispr-0.4.14_fix-imports.patch', + 'vispr-0.4.14_fix-yaml-load.patch', +] +checksums = [ + {'vispr-0.4.14.tar.gz': 'dc2cf6ac9c8930b0f1f1b3a2b7f57bfae180b2ac3674060123fd2d7fe10ccd82'}, + {'vispr-0.4.14_fix-imports.patch': '2744d5636ebd6849fb0fc99ff102a8a0256bec3e592c323c24132f1e694baf67'}, + {'vispr-0.4.14_fix-yaml-load.patch': '6b994103c621fafc084fc6c11f966367ffddc36ac20c0f9fc44ef0bb4360f977'}, +] + +dependencies = [ + ('Python', '3.10.4'), + ('Flask', '2.2.2'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('scikit-learn', '1.1.2'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/vispr'], + 'dirs': [], +} + +sanity_check_commands = ["vispr --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-imports.patch b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-imports.patch new file mode 100644 index 000000000000..162193ecf1c9 --- /dev/null +++ b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-imports.patch @@ -0,0 +1,26 @@ +fix import statement for pandas and Jinja2 +author: Denis Kristak (INUITS) + Kenneth Hoste (HPC-UGent) +diff -ru vispr-0.4.14.orig/vispr/results/rna.py vispr-0.4.14/vispr/results/rna.py +--- vispr-0.4.14.orig/vispr/results/rna.py 2016-08-11 09:16:23.000000000 +0200 ++++ vispr-0.4.14/vispr/results/rna.py 2023-04-10 19:19:07.488661966 +0200 +@@ -11,7 +11,7 @@ + + from flask import render_template + import pandas as pd +-from pandas.io.common import EmptyDataError ++from pandas.errors import EmptyDataError + import numpy as np + from sklearn.decomposition import PCA + from scipy.cluster.hierarchy import average, leaves_list, dendrogram +diff -ru vispr-0.4.14.orig/vispr/server.py vispr-0.4.14/vispr/server.py +--- vispr-0.4.14.orig/vispr/server.py 2015-11-08 00:47:23.000000000 +0100 ++++ vispr-0.4.14/vispr/server.py 2023-04-10 19:25:06.417148288 +0200 +@@ -10,7 +10,7 @@ + + import numpy as np + from flask import Flask, render_template, request, session, abort +-from jinja2 import Markup ++from markupsafe import Markup + import yaml + + from vispr import __version__ diff --git a/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-yaml-load.patch b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-yaml-load.patch new file mode 100644 index 000000000000..16d9b65d1a1f --- /dev/null +++ b/easybuild/easyconfigs/v/vispr/vispr-0.4.14_fix-yaml-load.patch @@ -0,0 +1,35 @@ +fix use of yaml.load, 'Loader' argument is required in PyYAML >= 6.0 +author: Kenneth Hoste (HPC-UGent) +diff -ru vispr-0.4.14.orig/vispr/cli.py vispr-0.4.14/vispr/cli.py +--- vispr-0.4.14.orig/vispr/cli.py 2017-02-15 14:38:22.000000000 +0100 ++++ vispr-0.4.14/vispr/cli.py 2023-04-10 19:26:01.251360284 +0200 +@@ -37,7 +37,7 @@ + print("Loading data.") + for path in configs: + with open(path) as f: +- config = yaml.load(f) ++ config = yaml.load(f, Loader=yaml.Loader) + try: + app.screens.add(config, parentdir=os.path.dirname(path)) + except KeyError as e: +@@ -91,7 +91,7 @@ + os.makedirs(directory) + + with open(configpath) as f: +- screen = Screen(yaml.load(f), parentdir=os.path.dirname(configpath)) ++ screen = Screen(yaml.load(f, Loader=yaml.Loader), parentdir=os.path.dirname(configpath)) + + def write(json, name): + with open(prefix + name + ".vega.json", "w") as out: +diff -ru vispr-0.4.14.orig/vispr/server.py vispr-0.4.14/vispr/server.py +--- vispr-0.4.14.orig/vispr/server.py 2015-11-08 00:47:23.000000000 +0100 ++++ vispr-0.4.14/vispr/server.py 2023-04-10 19:25:06.417148288 +0200 +@@ -20,7 +20,7 @@ + app.jinja_env.lstrip_blocks = True + + with open(os.path.join(os.path.dirname(__file__), "captions.yaml")) as f: +- CAPTIONS = yaml.load(f) ++ CAPTIONS = yaml.load(f, Loader=yaml.Loader) + + + @app.route("/ping") diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.3.1.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.3.1.eb new file mode 100644 index 000000000000..944357dedd6a --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.3.1.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'vsc-mympirun' +version = '5.3.1' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """mympirun is a tool to make it easier for users of HPC clusters to +run MPI programs with good performance.""" + +# we build this to work with every python version +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +use_pip = False + +exts_list = [ + ('setuptools', '41.6.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['6afa61b391dcd16cb8890ec9f66cc4015a8a31a6e1c2b4e0c464514be1a3d722'], + }), + ('future', '0.18.3', { + 'checksums': ['34a17436ed1e96697a86f9de3d15a3b0be01d8bc8de9c1dffd59fb8234ed5307'], + }), + ('pbr', '5.11.1', { + 'checksums': ['aefc51675b0b533d56bb5fd1c8c6c0522fe31896679882e1c4c63d5e4a0fccb3'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '5.0.2', { + 'checksums': ['06f18d7d65b44428202b145a9a36e99c2ee00d1eb992df0caf881d4664377891'], + }), + ('IPy', '1.01', { + 'modulename': 'IPy', + 'checksums': ['edeca741dea2d54aca568fa23740288c3fe86c0f3ea700344571e9ef14a7cc1a'], + }), + ('vsc-install', '0.18.5', { + 'modulename': 'vsc.install', + 'checksums': ['90e00ddde9d394fdb5426f6f4d466425c69acded3fdf25ce73a0b345f6afc036'], + }), + ('vsc-base', '3.5.3', { + 'modulename': 'vsc.utils', + 'checksums': ['7c4df43fc0508d6857acf8127deb1088b899cd364a14c688dac2d61617579ba9'], + }), + (name, version, { + 'modulename': False, + 'checksums': ['67fb89855044678e595fef39415aafdd26a1a9a4c89b3f89a4d34a1824df7bcf'], + }), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mypmirun', 'bin/mympisanity', 'bin/mytasks'], + 'dirs': ['bin/fake'], +} +sanity_check_commands = ["mympirun --help"] + +# can't enable 'pip check' since pip may not be installed in OS +sanity_pip_check = False + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb new file mode 100644 index 000000000000..68d5f0a82dff --- /dev/null +++ b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-11.2.0.eb @@ -0,0 +1,43 @@ +# Contribution from Imperial College London (UK) +# Uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'WCSLIB' +version = '7.11' + +homepage = 'https://www.atnf.csiro.au/people/mcalabre/WCS/' +description = """The FITS "World Coordinate System" (WCS) standard defines keywords +and usage that provide for the description of astronomical coordinate systems in a +FITS image header.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.atnf.csiro.au/pub/software/wcslib/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['46befbfdf50cd4953896676a7d570094dc7661e2ae9677b092e7fb13cee3da5f'] + +builddependencies = [ + ('binutils', '2.37'), + ('M4', '1.4.19'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('CFITSIO', '3.49'), + ('PGPLOT', '5.2.2'), + ('X11', '20210802'), +] + +configopts = '--with-cfitsiolib=$EBROOTCFITSIO/lib --with-cfitsioinc=$EBROOTCFITSIO/include ' +configopts += '--with-pgplotlib=$EBROOTPGPLOT/lib --with-pgplotinc=$EBROOTPGPLOT/include ' + +sanity_check_paths = { + 'files': ['bin/wcsgrid', 'bin/wcsware', 'lib/libpgsbox-7.11.a', 'lib/libpgsbox.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["wcsgrid --help 2>&1 | grep '^Usage: wcsgrid'"] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb new file mode 100644 index 000000000000..0a988032e846 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-21.1-intel-2021b.eb @@ -0,0 +1,77 @@ +name = 'WIEN2k' +version = '21.1' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +sources = ['%(name)s_%(version)s.tar'] +patches = [ + '%(name)s-%(version)s_fix_libxc_for_lapw0_mpi.patch', + '%(name)s-%(version)s_fix_system_stderr_redirection.patch', +] +checksums = [ + '32590778440a9280322bf2dc0d63f4f42a9fc48814fa6b8b7ee2d199c94bed11', # WIEN2k_21.1.tar + '1cc480a4824d9185ad5918dfc68c47bcb7826114626c8133d573be901bbdca84', # WIEN2k-21.1_fix_libxc_for_lapw0_mpi.patch + # WIEN2k-21.1_fix_system_stderr_redirection.patch + 'cdba467b0b6f2b310c2e1e2a3e6cabe75f8fd15ee0f7c14f8ef80c7e48073bdd', +] + +download_instructions = """ +WIEN2k can be ordered at http://susi.theochem.tuwien.ac.at/index.html. +""" + +dependencies = [ + ('Python', '3.9.6'), + ('Perl', '5.34.0'), + ('DFT-D3', '3.2.0'), + ('ELPA', '2021.05.001'), + ('FFTW', '3.3.10'), + ('libxc', '5.1.6'), +] + +osdependencies = [ + ('glibc-devel', 'libc6-dev'), # required for libpthread.a + ('tcsh'), # required by the installer +] + +# remote = 'pbsssh' +# If using a Slurm batch system it is highly recommended to use +# 'srun -n_NP_ _EXEC_' for wien_mpirun +wien_mpirun = 'mpirun -np _NP_ _EXEC_' +use_remote = False +mpi_remote = False +wien_granularity = True +taskset = 'no' + +# Change as needed, these are the defaults +# nmatmax = 19000 +# nume = 6000 + +fix_perl_shebang_for = [ + 'iniel_pressure_in2reader.pl_lapw', + 'iniel_pressure_reader.pl_lapw', + 'setrmt_lapw', + 'elast_setup_input.pl_lapw', + 'bashtime2csh.pl_lapw', +] + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1', r'^:ENE.*-1248.14']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*15.*total forces', + ]), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022b-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022b-dmpar.eb new file mode 100644 index 000000000000..a62a23d620c9 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4.1-foss-2022b-dmpar.eb @@ -0,0 +1,51 @@ +name = 'WRF' +version = '4.4.1' +buildtype = 'dmpar' +versionsuffix = '-%s' % buildtype + +homepage = 'https://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +source_urls = ['https://github.com/wrf-model/WRF/archive/'] +# sources = ['v%(version)s.tar.gz'] +sources = [{ + 'filename': 'v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/wrf-model', + 'repo_name': 'WRF', + 'tag': 'v%(version)s', + 'clone_into': 'WRF-%(version)s', + 'recursive': True, + }, +}] +patches = [ + 'WRF-4.4_netCDF-Fortran_separate_path.patch', +] +checksums = [ + None, # v4.4.1.tar.gz + '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch +] + +# csh is used by WRF install scripts +builddependencies = [ + ('Autotools', '20220317'), + ('tcsh', '6.24.07'), + ('time', '1.9'), + ('Perl', '5.36.0'), +] + +dependencies = [ + ('JasPer', '4.0.0'), + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb index 21b4362d798e..44897b5de17a 100644 --- a/easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20190717-GCCcore-8.3.0.eb @@ -31,6 +31,7 @@ builddependencies = [ ('gettext', '0.20.1'), ('pkg-config', '0.29.2'), ('intltool', '0.51.0'), + ('Doxygen', '1.8.16'), ] default_easyblock = 'ConfigureMake' diff --git a/easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb index 0c4398adb92b..ae81bf673627 100644 --- a/easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20200222-GCCcore-9.3.0.eb @@ -26,6 +26,7 @@ builddependencies = [ ('intltool', '0.51.0'), ('Meson', '0.55.1', '-Python-3.8.2'), ('Ninja', '1.10.0'), + ('Doxygen', '1.8.17'), ] dependencies = [ ('bzip2', '1.0.8'), diff --git a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb index d1a9f51ec07e..c5a69cfdb84e 100644 --- a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb @@ -26,6 +26,7 @@ builddependencies = [ ('intltool', '0.51.0'), ('Meson', '0.55.3'), ('Ninja', '1.10.1'), + ('Doxygen', '1.8.20'), ] dependencies = [ diff --git a/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb index b21040338545..e277989781ec 100644 --- a/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20210518-GCCcore-10.3.0.eb @@ -26,6 +26,7 @@ builddependencies = [ ('intltool', '0.51.0'), ('Meson', '0.58.0'), ('Ninja', '1.10.2'), + ('Doxygen', '1.9.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb index 259c0017c554..adc8a9e814be 100644 --- a/easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20210802-GCCcore-11.2.0.eb @@ -26,6 +26,7 @@ builddependencies = [ ('intltool', '0.51.0'), ('Meson', '0.58.2'), ('Ninja', '1.10.2'), + ('Doxygen', '1.9.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb index d417d954c4bd..0b3c1e7407bc 100644 --- a/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20220504-GCCcore-11.3.0.eb @@ -26,6 +26,7 @@ builddependencies = [ ('intltool', '0.51.0'), ('Meson', '0.62.1'), ('Ninja', '1.10.2'), + ('Doxygen', '1.9.4'), ] dependencies = [ diff --git a/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb index ea22050d1227..f98e6b15dbc0 100644 --- a/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb @@ -26,6 +26,7 @@ builddependencies = [ ('intltool', '0.51.0'), ('Meson', '0.64.0'), ('Ninja', '1.11.1'), + ('Doxygen', '1.9.5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.1-foss-2022a.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.1-foss-2022a.eb new file mode 100644 index 000000000000..36425089ffce --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.1-foss-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '1.7.1' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bb302c5c33e14bab94603940987940f29203ecb8767a7a719daf579fbfaace64'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# use the parallel parameter from EB instead of total procs in the system +preinstallopts = "sed -i 's/nproc = os.cpu_count.*$/nproc = %(parallel)s/' setup.py &&" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..ade6916dd58a --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.4.2' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['aa49909cbd9028c4666a35fa4975f9a6203ed98154fbb8223ee43ef9ceee97c3'] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.21.1', '', SYSTEM), + ('binutils', '2.40'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'], + 'dirs': [] +} + +sanity_check_commands = [ + "xz --help", + "unxz --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-13.1.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..ffee85b04a3d --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.4.2-GCCcore-13.1.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.4.2' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['aa49909cbd9028c4666a35fa4975f9a6203ed98154fbb8223ee43ef9ceee97c3'] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.21.1', '', SYSTEM), + ('binutils', '2.40'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'], + 'dirs': [] +} + +sanity_check_commands = [ + "xz --help", + "unxz --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb new file mode 100644 index 000000000000..262cfb87e362 --- /dev/null +++ b/easybuild/easyconfigs/x/xmlf90/xmlf90-1.5.6-GCC-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'xmlf90' +version = '1.5.6' + +homepage = 'https://gitlab.com/siesta-project/libraries/xmlf90' +description = """A fast XML parser and generator in Fortran""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/xmlf90/-/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c4492596c911b668b94fee40a53453f06aef3bc41014b9e2f4b51e640ad20528'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['lib/libxmlf90.a'], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/xmlf90'], +} + +runtest = 'test' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xxHash/xxHash-0.8.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/xxHash/xxHash-0.8.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..1cb665e60618 --- /dev/null +++ b/easybuild/easyconfigs/x/xxHash/xxHash-0.8.1-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'xxHash' +version = '0.8.1' + +homepage = 'https://cyan4973.github.io/xxHash' +description = "xxHash is an extremely fast non-cryptographic hash algorithm, working at RAM speed limit." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/Cyan4973/xxHash/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3bb6b7d6f30c591dd65aaaff1c8b7a5b94d81687998ca9400082c739a690436c'] + +builddependencies = [ + ('binutils', '2.39'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/xxhsum', 'include/xxh3.h', 'include/xxhash.h', + 'lib/libxxhash.a', 'lib/libxxhash.%s' % SHLIB_EXT, 'lib/pkgconfig/libxxhash.pc'], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["xxhsum --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..e09fb068964c --- /dev/null +++ b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'CMakeMake' +name = 'yaml-cpp' +version = '0.7.0' + +homepage = "https://github.com/jbeder/yaml-cpp" +description = """yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/jbeder/%(name)s/archive/'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-cmake-export.patch'] +checksums = [ + '43e6a9fcb146ad871515f0d0873947e5d497a1c9c60c58cb102a97b47208b7c3', + 'c562a575bbb161af478795e43bfd9073e3f874bea07134a321c1063cd7098c1c', # yaml-cpp-0.7.0_fix-cmake-export.patch +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3') +] + +sanity_check_paths = { + 'files': ['lib/libyaml-cpp.a', 'include/yaml-cpp/yaml.h'], + 'dirs': ['lib', 'include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/ZIMPL/ZIMPL-3.3.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/z/ZIMPL/ZIMPL-3.3.4-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..f193788ee275 --- /dev/null +++ b/easybuild/easyconfigs/z/ZIMPL/ZIMPL-3.3.4-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'MakeCp' + +name = 'ZIMPL' +version = '3.3.4' + +homepage = 'https://zimpl.zib.de/' +description = """ZIMPL is a little language to translate the mathematical model of a problem +into a linear or nonlinear (mixed-) integer mathematical program expressed in +.lp or .mps file format which can be read and (hopefully) solved by a LP or MIP +solver.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'scipopt' +source_urls = ['https://zimpl.zib.de/download/'] +sources = [SOURCELOWER_TGZ] +checksums = ['3362fb21524df459723d23f6e0c122ebdd684153a9cc991a2c7f5b2752a83eb2'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('GMP', '6.2.1'), + ('zlib', '1.2.12'), +] + +files_to_copy = ['bin', 'lib', (['src/*.h'], 'include/zimpl')] + +postinstallcmds = [ + "cd %(installdir)s/bin && ln -sf zimpl-%(version)s.* zimpl", + "cd %(installdir)s/lib && ln -sf libzimpl-%(version)s.*.a libzimpl.a", +] + +sanity_check_paths = { + 'files': ['bin/zimpl', 'lib/libzimpl.a'], + 'dirs': ['include/zimpl'], +} + +sanity_check_commands = ["zimpl -h"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..84708515be87 --- /dev/null +++ b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Zip' +version = '3.0' + +homepage = 'http://www.info-zip.org/Zip.html' +description = """Zip is a compression and file packaging/archive utility. +Although highly compatible both with PKWARE's PKZIP and PKUNZIP +utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives +have been portability and other-than-MSDOS functionality""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +checksums = ['f0e8bb1f9b7eb0b01285495a2699df3a4b766784c1765a8f1aeedf63c0806369'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" IZ_OUR_BZIP2_DIR=$EBROOTBZIP2 ' +buildopts += 'CFLAGS="$CFLAGS -I. -DUNIX -DBZIP2_SUPPORT -DUNICODE_SUPPORT -DLARGE_FILE_SUPPORT" ' +buildopts += 'generic_gcc' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/zip', 'bin/zipcloak', 'bin/zipnote', 'bin/zipsplit'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["zip --version"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..ff3257294a75 --- /dev/null +++ b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Zip' +version = '3.0' + +homepage = 'http://www.info-zip.org/Zip.html' +description = """Zip is a compression and file packaging/archive utility. +Although highly compatible both with PKWARE's PKZIP and PKUNZIP +utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives +have been portability and other-than-MSDOS functionality""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +checksums = ['f0e8bb1f9b7eb0b01285495a2699df3a4b766784c1765a8f1aeedf63c0806369'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" IZ_OUR_BZIP2_DIR=$EBROOTBZIP2 ' +buildopts += 'CFLAGS="$CFLAGS -I. -DUNIX -DBZIP2_SUPPORT -DUNICODE_SUPPORT -DLARGE_FILE_SUPPORT" ' +buildopts += 'generic_gcc' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/zip', 'bin/zipcloak', 'bin/zipnote', 'bin/zipsplit'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["zip --version"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..b139a83d3cda --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.13' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +# patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch'] +checksums = ['b3a24de97a8fdbc835b9833169501030b8977031bcb54b3b3ac13740f846ab30'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.40', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.1.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.1.0.eb new file mode 100644 index 000000000000..082092433d1f --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.13-GCCcore-13.1.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.13' + +homepage = 'https://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '13.1.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils'] +sources = [SOURCELOWER_TAR_GZ] +# patches = ['zlib-%(version)s_fix-CC-logic-in-configure.patch'] +checksums = ['b3a24de97a8fdbc835b9833169501030b8977031bcb54b3b3ac13740f846ab30'] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.40', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb new file mode 100644 index 000000000000..397dbe63b578 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.13' + +homepage = 'https://www.zlib.net/' + +description = """ + zlib is designed to be a free, general-purpose, legally unencumbered -- that + is, not covered by any patents -- lossless data-compression library for use + on virtually any computer hardware and operating system. +""" + +toolchain = SYSTEM +toolchainopts = {'pic': True} + +source_urls = ['https://zlib.net/fossils/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b3a24de97a8fdbc835b9833169501030b8977031bcb54b3b3ac13740f846ab30'] + +# need to take care of $CFLAGS ourselves with dummy toolchain +# we need to add -fPIC, but should also include -O* option to avoid +# compiling with -O0 (default for GCC) +buildopts = 'CFLAGS="-O2 -fPIC"' + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', + 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.9.eb b/easybuild/easyconfigs/z/zsh/zsh-5.9.eb new file mode 100644 index 000000000000..5c8ea48d53c1 --- /dev/null +++ b/easybuild/easyconfigs/z/zsh/zsh-5.9.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'zsh' +version = '5.9' + +homepage = 'https://www.zsh.org/' +description = "Zsh is a shell designed for interactive use, although it is also a powerful scripting language." + +toolchain = SYSTEM + +source_urls = ['https://prdownloads.sourceforge.net/%(namelower)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['9b8d1ecedd5b5e81fbf1918e876752a7dd948e05c1a0dba10ab863842d45acd5'] + +osdependencies = [ + ('ncurses-devel', 'libncurses-dev'), +] + +configopts = '--with-tcsetpgrp' # needed to build in non-login shells + +modextrapaths = {'FPATH': 'share/zsh/%(version)s/functions'} + +sanity_check_paths = { + 'files': ['bin/zsh'], + 'dirs': ['lib/zsh/%(version)s', 'share'], +} + +sanity_check_commands = ['zsh --version'] + +# optionally make this module sticky (lmod only): +# modluafooter = 'add_property("lmod", "sticky")' + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.5.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/zstd/zstd-1.5.5-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..dda0d74b1748 --- /dev/null +++ b/easybuild/easyconfigs/z/zstd/zstd-1.5.5-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'zstd' +version = '1.5.5' + +homepage = 'https://facebook.github.io/zstd' +description = """Zstandard is a real-time compression algorithm, providing high compression ratios. + It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. + It also offers a special mode for small data, called dictionary compression, and can create dictionaries + from any sample set.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'facebook' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['98e9c3d949d1b924e28e01eccb7deed865eefebf25c2f21c702e5cd5b63b85e1'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('gzip', '1.12'), + ('XZ', '5.4.2'), + ('lz4', '1.9.4'), +] + +skipsteps = ['configure'] + +runtest = 'check' + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ["bin/zstd", "lib/libzstd.%s" % SHLIB_EXT, "include/zstd.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/setup.py b/setup.py index 3820ff609f15..70004ce1b127 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.7.1' +VERSION = '4.7.2' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 9e2523ae1b98..4e9b5508fd73 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1124,14 +1124,15 @@ def test_pr_sanity_check_paths(self): """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" # some generic easyblocks already have a decent customised sanity_check_paths, - # including CMakePythonPackage, GoPackage, JuliaBundle, PythonBundle & PythonPackage; + # including CargoPythonPackage, CMakePythonPackage, GoPackage, JuliaBundle, PythonBundle & PythonPackage; # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. - whitelist = ['BuildEnv', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', 'JuliaBundle', 'ModuleRC', - 'PythonBundle', 'PythonPackage', 'Toolchain'] + whitelist = ['BuildEnv', 'CargoPythonPackage', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', + 'JuliaBundle', 'ModuleRC', 'PythonBundle', 'PythonPackage', 'Toolchain'] # Bundles of dependencies without files of their own # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, - # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co - bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle', 'ROCm'] + # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co, + # Python-bundle: Python + SciPy-bundle + matplotlib + JupyterLab + bundles_whitelist = ['Autotools', 'CESM-deps', 'CUDA', 'GCC', 'FEniCS', 'ESL-Bundle', 'Python-bundle', 'ROCm'] failing_checks = []