[Bio-packaging] Packaging

[Ricardo Wurmus]

> I like GNU Guix and Docker because they are Linux distribution
> agnostic. They both require Linux, but I don't think that really is a
> problem. Deployment for me (at this stage) is mostly about batch
> processing on Linux clusters. I run Debian, but I also have to work on
> CentOS. Agnostic is good (here). 
>
> Ricardo has been working on GNU Guix packaging for bioinformatics and
> he has a nice writeup here:
>
>   http://elephly.net/posts/2015-04-17-gnu-guix.html

I'd like to note that one of the primary things using GNU Guix gives you
(almost) for free is reproducibility.  This is a very important property
when it comes to reproducing published results and, I think, publishing
results.  With Guix it is possible to freeze whole workflow networks at
particular versions without affecting software environments of other
users --- or even of the very same user e.g. for a different project.

I'm still packaging new bioinformatics and machine-learning packages for
Guix every week; the latest additions are Couger and a minimal version
of BioPerl.  Next week I'll be presenting Guix to another group of
system administrators at an associated institute as they are currently
looking for a software management solution for their new cluster.

> Also Debian packaging does not resolve dependencies,
> reproducibility, nor versioning. RPM is in that same boat, so I have
> not even tried that.

I used to manage a separate RPM repository for part of the institute and
I'm glad the move to Guix was painless.  RPM packaging is time consuming
and feels like a waste of time considering that the resulting binaries
aren't portable, aren't relocatable without additional effort, cannot be
installed in user package databases in *addition* to whatever is
available in the host system ... It's a step up from build-and-forget
deployments but it's hardly worth the effort.

Guix is completely self-contained, so we're using it on Ubuntu and
CentOS cluster nodes, through a shared network share.  We're also
experimenting with sharing software with unmanaged workstations.  As
long as they run GNU/Linux this usually just works.

~~ Ricardo