From mboxrd@z Thu Jan  1 00:00:00 1970
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Subject: Re: [PATCH] gnu: Add freebayes
Date: Mon, 2 May 2016 17:21:29 +0200
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To: Rob Syme <rob.syme@gmail.com>
Cc: guix-devel@gnu.org


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=E2=80=99t 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