Reproducible Software

Report

GNU Guix is a software packaging system that allows for full control of the dependency graph and therefor reproducible software installations. The aim in this biohackathon was to have Docker work with Guix for deployment on (for example) Arvados. Examples are from Nix, Bruno and Raoul.

We wrote documentation and new software packages for CWL, Ruby and R. The following packages were added during the hackathon:

ruby-bio-logger
ruby-cucumber-core
ruby-log4r
ruby-gherkin3
ruby-bio-blastxmlparser
bio-locus
r-qtl
mafft

We also started preparing for software discovery. Guix comes with a continuous integration system on a build farm. We want to harvest that information to see when packages are building or failing. See, for example, the Ruby builds.

Support for perl (397 packages), python (296), ruby (47), and R (54) is growing fast. At this point there are also 56 bioinformatics packages: aragorn, bamtools, bedops, bedtools, bio-locus, bioperl-minimal, blast+, bowtie, bwa, clipper, clustal-omega, couger, crossmap, cutadapt, deeptools, diamond, edirect, express, fasttree, fastx-toolkit, flexbar, grit, hisat, hmmer, htseq, htsjdk, htslib, idr, macs, mafft, metabat, miso, ncbi-vdb, ngs-java, ngs-sdk, orfm, pbtranscript-tofu, plink, preseq, prodigal, python2-biopython, python2-bx-python, python2-pbcore, python2-pybedtools, python2-warpedlmm, python-biopython, r-qtl, rsem, rseqc, samtools, samtools-0.1, seqan, sra-tools, star, subread, and vcftools.