Re: [PATCH] gnu: Add freebayes

[Rob Syme]

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 <address@hidden> wrote:

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