From: Leo Famulari <leo@famulari.name>
To: Pjotr Prins <pjotr.public12@thebird.nl>
Cc: guix-devel@gnu.org
Subject: Re: [PATCH] gnu: Add freebayes.
Date: Wed, 9 Mar 2016 02:31:58 -0500 [thread overview]
Message-ID: <20160309073158.GA24805@jasmine> (raw)
In-Reply-To: <20160309065320.GB16207@thebird.nl>
On Wed, Mar 09, 2016 at 07:53:20AM +0100, Pjotr Prins wrote:
> On Tue, Mar 08, 2016 at 04:44:13PM +0100, Roel Janssen wrote:
> > One of the problems with the patch is probably the bulk of dependencies
> > dragged in (for example, vcflib). They use specific versions so they
> > are tied to this package (so that's why I cannot package them separately).
>
> This approach is very common in bioinformatics and one way they fight
> dependency hell. Not the best way, admittedly.
>
> It may be worthwhile to package vcflib, for example, separately as
> freebayes merely requires the header files to compile. The problem is
> that that te current vcflib does not include the headers from a
> default install, if I understand Roel correctly. Ricardo, can you
> advice on this? Should we add the headers in guix through a vcflib
> installer?
>
> Personally I favour adding freebayes as is and when we decide to
> package these libraries separately revisit the issues.
Okay, I'm fine with the approach. It does make sense if these specific
versions only make sense in this particular context. And you are the
experts in bioinformatics software, not me :)
Ricardo, your thoughts?
next prev parent reply other threads:[~2016-03-09 7:32 UTC|newest]
Thread overview: 13+ messages / expand[flat|nested] mbox.gz Atom feed top
2016-03-08 15:44 [PATCH] gnu: Add freebayes 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 [this message]
2016-03-10 9:56 ` Roel Janssen
2016-03-09 10:17 ` Ricardo Wurmus
-- strict thread matches above, loose matches on Subject: below --
2016-05-02 9:25 Rob Syme
2016-05-02 15:21 ` Ricardo Wurmus
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
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