[Bio-packaging] GNU Guix update

[Pjotr Prins]

It has been a while, time for another update. Great news is that we
have Docker and CWL support!

** Biohackathon Nagasaki Japan 2015 Report

[GNU Guix](https://www.gnu.org/software/guix/) is a software packaging
system that allows for full control of the dependency graph and
therefore reproducible software installations.

## Docker with Guix

The aim in this biohackathon was to have Docker work with Guix for
deployment on (for example) Arvados. Examples are from
[Nix](https://github.com/datakurre/nix-build-pack-docker),
[Bruno](https://github.com/bmpvieira/Dockerfiles/tree/master/guix) and
Raoul. With the Guix version there is still a catch that it requires
priviliges for the daemon. The Nix version, however, shows that it can
do without if started as a normal user.

## New packages

We wrote new packages for Guix and
[documentation](https://github.com/pjotrp/guix-notes/) for
packaging/hacking Guix and Rubygems. 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](http://hydra.gnu.org/job/gnu/master/ruby-2.2.3.x86_64-linux)
which contain the SHA values of the package as well as the checkout of
the Guix git repository reflecting the exact dependency graph.  We are
collaborating with Nix and Guix communities to get this information as
JSON output so it can be used in a web-service.

Support for perl (397 packages), python (296), ruby (47), and R (54)
with GNU Guix is growing fast. 

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.