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Merge pull request #17985 from easybuilders/4.7.x
release EasyBuild v4.7.2
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| ## | ||
| # This is a contribution from SIB Swiss Institute of Bioinformatics | ||
| # Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it | ||
| # | ||
| # Authors:: Sebastien Moretti <sebastien.moretti@sib.swiss> | ||
| # | ||
| ## | ||
|
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| # JAR files are in a subdirectory with other stuff, so use Binary | ||
| easyblock = 'Binary' | ||
|
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| name = 'AGeNT' | ||
| version = '3.0.6' | ||
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| 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.""" | ||
|
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| software_license = 'LicenseVeryRestrictive' | ||
| # For Research Use Only. Not for use in diagnostic procedures. | ||
|
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| toolchain = SYSTEM | ||
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| builddependencies = [ | ||
| ('UnZip', '6.0', '', ('GCCcore', '10.3.0')), | ||
| ] | ||
| dependencies = [ | ||
| ('Java', '11'), | ||
| ] | ||
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| # Fill the form at https://explore.agilent.com/AGeNT-Software-Download-Form | ||
| # to get the zip file. | ||
| sources = ['AGeNT_%(version)s.zip'] | ||
| checksums = ['746e4445567ee41b7ced5cab3cd252d27d8f6f9eab56766e5d7ca74894e3db73'] | ||
|
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| extract_sources = False | ||
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| 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' | ||
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| sanity_check_paths = { | ||
| 'files': ['bin/agent.sh'], | ||
| 'dirs': ['bin', 'lib'] | ||
| } | ||
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| sanity_check_commands = ["agent.sh"] | ||
|
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| moduleclass = 'bio' |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,63 @@ | ||
| easyblock = 'PythonBundle' | ||
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| name = 'ASE' | ||
| version = '3.22.1' | ||
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| 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.""" | ||
|
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| toolchain = {'name': 'gfbf', 'version': '2022b'} | ||
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| 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 | ||
| ] | ||
|
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| use_pip = True | ||
| sanity_pip_check = True | ||
|
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| 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'], | ||
| }), | ||
| ] | ||
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| sanity_check_paths = { | ||
| 'files': ['bin/ase'], | ||
| 'dirs': ['lib/python%(pyshortver)s/site-packages'], | ||
| } | ||
|
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| # make sure Tkinter is available, otherwise 'ase gui' will not work | ||
| sanity_check_commands = ["python -c 'import tkinter' "] | ||
|
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| moduleclass = 'chem' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| easyblock = 'PythonBundle' | ||
|
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| name = 'ASE' | ||
| version = '3.22.1' | ||
|
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| 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.""" | ||
|
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| toolchain = {'name': 'gomkl', 'version': '2021a'} | ||
|
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| 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 | ||
| ] | ||
|
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| use_pip = True | ||
| sanity_pip_check = True | ||
|
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| exts_list = [ | ||
| ('pytest-mock', '3.6.1', { | ||
| 'checksums': ['40217a058c52a63f1042f0784f62009e976ba824c418cced42e88d5f40ab0e62'], | ||
| }), | ||
| ('ase', version, { | ||
| 'checksums': ['004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'], | ||
| }), | ||
| ('ase-ext', '20.9.0', { | ||
| 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], | ||
| }), | ||
| ] | ||
|
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| sanity_check_paths = { | ||
| 'files': ['bin/ase'], | ||
| 'dirs': ['lib/python%(pyshortver)s/site-packages'], | ||
| } | ||
|
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| # make sure Tkinter is available, otherwise 'ase gui' will not work | ||
| sanity_check_commands = ["python -c 'import tkinter' "] | ||
|
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| moduleclass = 'chem' |
31 changes: 31 additions & 0 deletions
31
easybuild/easyconfigs/a/Abseil/Abseil-20230125.2-GCCcore-12.2.0.eb
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| Original file line number | Diff line number | Diff line change |
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| easyblock = 'CMakeMake' | ||
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| name = 'Abseil' | ||
| version = '20230125.2' | ||
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| 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.""" | ||
|
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| toolchain = {'name': 'GCCcore', 'version': '12.2.0'} | ||
| toolchainopts = {'pic': True, 'cstd': 'c++17'} | ||
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| source_urls = ['https://github.com/abseil/abseil-cpp/archive/refs/tags'] | ||
| sources = ['%(version)s.tar.gz'] | ||
| checksums = ['9a2b5752d7bfade0bdeee2701de17c9480620f8b237e1964c1b9967c75374906'] | ||
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| builddependencies = [ | ||
| ('binutils', '2.39'), | ||
| ('CMake', '3.24.3'), | ||
| ] | ||
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| configopts = '-DBUILD_SHARED_LIBS=ON ' | ||
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| sanity_check_paths = { | ||
| 'files': ['lib/libabsl_base.%s' % SHLIB_EXT], | ||
| 'dirs': ['include/absl'], | ||
| } | ||
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| moduleclass = 'lib' |
31 changes: 31 additions & 0 deletions
31
easybuild/easyconfigs/a/Abseil/Abseil-20230125.3-GCCcore-12.3.0.eb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| easyblock = 'CMakeMake' | ||
|
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| name = 'Abseil' | ||
| version = '20230125.3' | ||
|
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| 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.""" | ||
|
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| toolchain = {'name': 'GCCcore', 'version': '12.3.0'} | ||
| toolchainopts = {'pic': True, 'cstd': 'c++17'} | ||
|
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| source_urls = ['https://github.com/abseil/abseil-cpp/archive/refs/tags'] | ||
| sources = ['%(version)s.tar.gz'] | ||
| checksums = ['5366d7e7fa7ba0d915014d387b66d0d002c03236448e1ba9ef98122c13b35c36'] | ||
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| builddependencies = [ | ||
| ('binutils', '2.40'), | ||
| ('CMake', '3.26.3'), | ||
| ] | ||
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| configopts = '-DBUILD_SHARED_LIBS=ON ' | ||
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| sanity_check_paths = { | ||
| 'files': ['lib/libabsl_base.%s' % SHLIB_EXT], | ||
| 'dirs': ['include/absl'], | ||
| } | ||
|
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| moduleclass = 'lib' |
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