Re: [PATCH] gnu: Add freebayes

[Roel Janssen <roel@gnu.org>]

Hello Rob,

Actually, at the time I packaged freebayes, I intended to use the
recursive Git fetch, but there was a problem with it in Guix at that
moment.

So, the clutter in my package should do almost the same as the Git
recursive fetch :).

There are still some licensing problems with freebayes.  First, we need
to get vcflib in Guix, for which the following needs to be resolved:
- fastahack:  No free/open source license.
- smithwaterman: No free/open source license.
- tabixpp: No free/open source license.

For the other dependencies, I sent packages to the list.  Some made it
in upstream already (filevercmp), and other are still in review.  For
the three packages mentioned above we must first resolve the licensing
issues.

I sent Erik an e-mail a week ago asking to add licenses to these
projects, and he told me he will look into this soon.  Feel free to keep
reminding him to look into this :).

Kind regards,
Roel Janssen


Rob Syme writes:

> 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 <ricardo.wurmus@mdc-berlin.de>
> wrote:
>
>>
>> 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
>>