Re: [PATCH] gnu: Add freebayes

[Rob Syme <rob.syme@gmail.com>]

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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
>

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