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Re: [PATCH] gnu: Add freebayes
From: |
Ricardo Wurmus |
Subject: |
Re: [PATCH] gnu: Add freebayes |
Date: |
Mon, 2 May 2016 17:21:29 +0200 |
Hi Rob,
> A guix-friendly licensed variant caller.
>
> From 78fb1be26ca1a0ac768ce5b98f7fd9f467870b84 Mon Sep 17 00:00:00 2001
> From: Rob Syme <address@hidden>
> 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