[Bio-packaging] GNU Guix update

[Ricardo Wurmus]

> At this point there are 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.

A searchable package list can also be found here:

    http://guix.mdc-berlin.de

You can search for “bioinfo” and all packages in the bioinformatics
module should be displayed.  There are also some machine learning
packages and statistics packages that are used in bioinformatics, but
are not located in this module.

In addition to the update Pjotr posted I’d like to mention that there is
a dedicated build system for R packages and an importer for CRAN
packages.  Creating a Guix package expression from a CRAN package
(e.g. DBI) now takes little more than this:

    guix import cran DBI

The output is an expression that takes very little editing can be bound
to a variable in statistics.scm.  To add the package to Guix upstream
then only requires submitting a simple patch to guix-devel at gnu.org.

~~ Ricardo