[Bio-packaging] testing out guix

[Ricardo Wurmus]

Hi Malcolm,

> 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.

Oh, great to read that it reached someone who might benefit from it :)

> 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):>

[...]

I just went through the list and found a few that looked familiar.
Below are some comments.

Non-free, won't package:

> gatk
> jimKentUtils

On my list (possibly non-free):

> igv
> igvtools
> meme
> picard (requires more Java toolchain stuff to build from source)
> soapdenovo2
> trimmomatic

Non-free stuff, packaged in my private guix-nonfree repo:

> macs14
> tophat
> viennaRNA

Free stuff, packaged and available through Guix:

> bamtools
> bedtools
> blast+  (WIP, it's really big)
> bowtie2
> cufflinks
> fastqc
> fastx_toolkit
> graphviz
> ncbi_sra_toolkit
> ngsutils
> rsem
> star
> tabix

These look familiar but I'm not sure if I already have them:

> bam2fastq
> bcftools

[...]

> Gonna be a party!

Indeed!  I would be very happy if you decide for Guix in the end.  There
isn't a lot of bioinfo stuff there yet, but that can be fixed by having
more people contribute recipes.

Cheers,
Ricardo