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From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: Rob Syme <rob.syme@gmail.com>
Cc: guix-devel@gnu.org
Subject: Re: [PATCH] gnu: Add freebayes
Date: Mon, 2 May 2016 17:21:29 +0200	[thread overview]
Message-ID: <idjfuu05vuu.fsf@bimsb-sys02.mdc-berlin.net> (raw)
In-Reply-To: <CAEf4xgdco--bDzV0gw=FJEkEQ+dSPssmbosfA7XNHofRtJKm6w@mail.gmail.com>


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

  reply	other threads:[~2016-05-02 15:22 UTC|newest]

Thread overview: 13+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2016-05-02  9:25 [PATCH] gnu: Add freebayes Rob Syme
2016-05-02 15:21 ` Ricardo Wurmus [this message]
2016-05-03  7:32   ` Rob Syme
2016-05-03  7:45     ` Roel Janssen
2016-05-03  7:52       ` Rob Syme
2016-05-03 12:34         ` Pjotr Prins
  -- strict thread matches above, loose matches on Subject: below --
2016-03-08 15:44 Roel Janssen
2016-03-08 23:55 ` Leo Famulari
2016-03-09  6:44   ` Pjotr Prins
2016-03-09  6:53 ` Pjotr Prins
2016-03-09  7:31   ` Leo Famulari
2016-03-10  9:56     ` Roel Janssen
2016-03-09 10:17 ` Ricardo Wurmus

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