Ah. Good point Roel. Until the licencing is resolved, any discussion about
how to package freebayes is of no practical value. I'll ping Erik about the
licencing as well :)
-r

P.S. Erik's latest biorxiv preprint is worth a read (A Graph Extension of
the Positional Burrows-Wheeler Transform and its Applications):
http://biorxiv.org/content/early/2016/05/02/051409

On Tue, 3 May 2016 at 15:46 Roel Janssen <roel@gnu.org> wrote:

> Hello Rob,
>
> Actually, at the time I packaged freebayes, I intended to use the
> recursive Git fetch, but there was a problem with it in Guix at that
> moment.
>
> So, the clutter in my package should do almost the same as the Git
> recursive fetch :).
>
> There are still some licensing problems with freebayes.  First, we need
> to get vcflib in Guix, for which the following needs to be resolved:
> - fastahack:  No free/open source license.
> - smithwaterman: No free/open source license.
> - tabixpp: No free/open source license.
>
> For the other dependencies, I sent packages to the list.  Some made it
> in upstream already (filevercmp), and other are still in review.  For
> the three packages mentioned above we must first resolve the licensing
> issues.
>
> I sent Erik an e-mail a week ago asking to add licenses to these
> projects, and he told me he will look into this soon.  Feel free to keep
> reminding him to look into this :).
>
> Kind regards,
> Roel Janssen
>
>
> Rob Syme writes:
>
> > Hi Ricardo
> >
> > I'm sorry for not checking the list beforehand! Interestingly, we ended
> up
> > with very different solutions to the problem of including the freebayes
> > dependencies. Using the recursive git fetch compiles without issue for me
> > and *seems* to produce sensible results. Perhaps some non-guix packages
> are
> > bleeding in from my configuration? If so, any verification that it
> > works/breaks would be appreciated. If it *does* work, I'd argue that
> using
> > "(recursive? #t)" is a neater and more upgradable solution to the problem
> > of the freebayes git submodule problem, as we wouldn't need to update the
> > hashes and urls for bamtools-src, vcflib-src, tabixpp-src, etc.
> >
> > On Mon, 2 May 2016 at 23:21 Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de
> >
> > wrote:
> >
> >>
> >> Hi Rob,
> >>
> >> > A guix-friendly licensed variant caller.
> >> >
> >> > From 78fb1be26ca1a0ac768ce5b98f7fd9f467870b84 Mon Sep 17 00:00:00 2001
> >> > From: Rob Syme <rob.syme@gmail.com>
> >> > Date: Mon, 2 May 2016 16:46:53 +0800
> >> > Subject: [PATCH] gnu: Add freebayes
> >> >
> >> > * gnu/packages/bioinformatics.scm (freebayes): New variable.
> >> >
> >> > ---
> >>
> >> thanks for the patch!  I see that freebayes has a couple of git
> >> submodules, e.g. for bamtools, intervaltree, and vcflib.  I remember
> >> Roel was working on this before, trying to untangle all the
> >> dependencies.
> >>
> >> See this discussion here:
> >>
> >>     http://lists.gnu.org/archive/html/guix-devel/2016-03/msg00333.html
> >>
> >> I don’t see any special treatment of these dependencies in your
> >> package.  Is this not needed?  Or does the git checkout include all the
> >> bundled dependencies?
> >>
> >> I think we should use one of the release tarballs instead and make sure
> >> to package the dependencies separately.  Maybe you can cooperate with
> >> Roel, who has made a lot of progress on this end already.
> >>
> >> What do you think?
> >>
> >> ~~ Ricardo
> >>
>
>