[Bio-packaging] testing out guix

[Cook, Malcolm]

Ricardo,

Pleased to e-meet you.  It was your http://elephly.net/posts/2015-04-17-gnu-guix.html that got on this path.  I'm so glad I found it.  

For my bioinformatics core  facility I've been trying out various approaches to dishing science apps to all comers with minimal headache.  I've been test driving spack, and before that EasyBuild with modules/lmod.  I javen't yet made the final commit, but, I think guix is going to serve my needs quite well.  Plus I'm a lisp-er from the 80's so staring at Guile brings me nicely back.

> > Agreed, but, I don't yet understand how such effort relates to either of:
> >
> >
> 	http://git.savannah.gnu.org/cgit/guix.git/tree/gnu/packages/bioinfo
> rmatics.scm
> >
> >
> https://github.com/BIMSBbioinfo/guix/blob/master/gnu/packages/bioinfor
> > matics.scm
> >
> > Do you?  Are these other people with similar intention?  Are they
> > already on board with you, or, vice versa?
> 
> I know this has been answered already, but I thought I'd add some info
> about these two.

Thanks for the clarification.

> The second used to be an outdated clone for use at the institute which pays
> me.  I have removed it a few hours ago to avoid confusion as the repository is
> no longer used.

Poof!  Redundancy gone!  Clarity prevails!  Thanks!

> The first---the bioinformatics module of GNU Guix upstream---is where we
> would ideally add package definitions for free/libre bioinformatics software.
> Ben's package definition for OrfM, for example, will arrive there momentarily
> as I submitted it to the guix-devel mailing list as a patch and it has already
> passed review.  I have commit access to the GNU Guix git repository on
> Savannah, but we usually first expose the patches to the mailing list for a
> quick review.

Great.  I have a trove of recipes (in either bash and a brew-derivative) which I intend to move into guix over time, unless I'm beaten to any of them (I'm sure I already have been for some):

abyss
amos
bam2fastq
bam_stats
bamtools
bcftools
bedtools
bioawk
bismark
blast+
#blat - as part of jimKentUtils
bowtie2
bpipe
circos
cufflinks
cytoscape
ensembl_perl
epcr
fastqc
fastx_toolkit
gapcloser
gatk
ggobi
go
graphviz
hmmer
igv
igvtools
io_lib # from staden
jellyfish
jimKentUtils
locarna
macs14
meme
mfold
mfold_util
miranda
mirdeep2
MUMmer3.23
muscle
ncbi_sra_toolkit
neuroscope
ngsutils
novocraft
parallel
philGreenUtils
picard
pigz
primer3
pymol
relocate
RNAz
rsem
seqtk
sge
snpeff
snpomatic
soapdenovo2
sparsehash
ssaha_pileup
sshpass
staden
star
tabix
tophat
trimmomatic
trinity
velvet
viennaRNA
wublast


I'll have to review the licenses on each as I go.... and try and winnow out the list a bit too (there is a bunch of "old school" cruft there).

Oh, and a handful of non-free too:  aspera-ascp, Mathematica, matlab, 

Gonna be a party!

~Malcolm 

> 
> ~~ Ricardo