[Bio-packaging] GNU Guix update

[Pjotr Prins]

Time for an half-yearly update on GNU Guix. A lot has been going on
and using Guix has become a pretty slick experience. We are deploying
Guix in multiple bioinformatics computing environments now. I predict 
GNU Guix is going to get major coverage in 2016.

Since my last message in july the number of packages went up for Ruby
to 110 (from 47), R 107 (from 54) and python 426 (from 296). All
binaries are at the most recent versions of the interpreters.
Julia and D-language support has been added and 74 packages are
bioinformatics related (see below).

GNU Guix is the only certifiable solution for reproducible deployment
that I know. If you want to read up on Docker concerns, this is a good one:

- Link http://www.vitavonni.de/blog/201503/2015031201-the-sad-state-of-sysadmin-in-the-age-of-containers.html

In the coming months we are going to keep on adding tools for NGS,
including snv and sv callers. Roel Janssen is going to spend dedicated 
time on that. 

Happy Hacking in 2016.

Current packages include (note the two samtools versions):

aragorn 1.2.36, bamtools 2.3.0, bedops 2.4.14, bedtools 2.24.0,
bio-blastxmlparser 2.0.4, bio-locus 0.0.7, bioperl-minimal 1.6.924,
bioruby 1.5.0, blast+ 2.2.31, bless 1p02, bowtie 2.2.4, bwa 0.7.12,
clipper 0.3.0, clustal-omega 1.2.1, couger 1.8.2, crossmap 0.2.1,
cutadapt 1.8, deeptools 1.5.11, diamond 0.7.9, edirect 2.50, express
1.5.1, express-beta-diversity 1.0.7, fasttree 2.1.8, fastx-toolkit
0.0.14, flexbar 2.5, grit 2.0.2, hisat 0.1.4, hmmer 3.1b2, htseq
0.6.1, htsjdk 1.129, htslib 1.2.1, idr 2.0.0, macs 2.1.0.20140616,
mafft 7.267, metabat 0.26.1, miso 0.5.3, mosaik 2.2.30, ncbi-vdb
2.5.4, ngs-java 1.2.2, ngs-sdk 1.2.2, orfm 0.4.1, pbtranscript-tofu
2.2.3.8f5467fe6, plink 1.07, preseq 2.0, prodigal 2.6.2,
python-biopython 1.66, python2-biopython 1.66, python2-bx-python
0.7.2, python2-pbcore 0.9.3, python2-pybedtools 0.6.9,
python2-warpedlmm 0.21, r-acsnminer 0.15.11, r-biocgenerics 0.16.1,
r-genomeinfodb 1.6.1, r-genomicranges 1.22.2, r-iranges 2.4.6, r-qtl
1.37-11, r-s4vectors 0.8.5, r-xvector 0.10.0, rsem 1.2.20, rseqc
2.6.1, ruby-bio-logger 1.0.1, samtools 0.1.19, samtools 1.2, seqan
1.4.2, seqmagick 0.6.1, smithlab-cpp 0.1.728a097, snap-aligner
1.0beta.18, sra-tools 2.5.4, star 2.4.2a, subread 1.4.6-p2, vcftools
0.1.12b, vsearch 1.4.1.