[Bio-packaging] testing out guix

[Ricardo Wurmus]

> I think I might have run out of time for getting this patch ready in the 
> correct format. This one works from my own one, I'm guessing it works 
> when patched in, you are welcome to it.

Thank you for the patch!  I'll add it to the bioinformatics module and
attribute it to you.

> I'm thinking that the mailing list method is foreign to most 
> bioinformaticians so a github for collating them would be useful, yeh.

I'll see if maybe I can set up a regularly synced github mirror for
contributors who are uncomfortable with sending patches to the mailing
list.  (I prefer this method over Github pull requests, but I realise
others have a different opinion on this.)

> One thing that I'm trying to understand. Is there any way you can 
> configure guix to be able to serve different versions of the same 
> software a la module systems on clusters? I'm told there's a video at 
> http://www.gnu.org/software/guix/ where at the end someone asks this 
> question and the presenter effectively says no to this.

Yes, it is possible to define package variables for different versions
of one software.  Currently in bioinformatics.scm we have two versions
of Samtools, for example.  It is possible to have more than two
versions, but there would need to be a good reason to keep them upstream
in GNU Guix.  It is totally feasible, though, to have a separate
repository with as many legacy versions as you wish.  In fact, I
maintain a repository with recipes that I don't intend to upstream to
GNU Guix, which contains various legacy versions that are of interest to
our users here, but are not suitable for submission to Guix upstream.

To install multiple versions you have to consider clobbering.  Samtools
for example provides $out/bin/samtools in version 0.1.19 as well as in
1.1, so you cannot install both of these binaries into the very same
profile.  With Guix you can target profiles simply by passing "-p
/path/to/new/profile" to "guix package", e.g.:

    guix package -p my-pipeline -i samtools-0.1.19 macs

~~ Ricardo