From mboxrd@z Thu Jan 1 00:00:00 1970 From: Rob Syme Subject: Re: [PATCH] gnu: Add freebayes Date: Tue, 03 May 2016 07:32:32 +0000 Message-ID: References: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=089e01538ac84cd6d30531eb1da6 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:60305) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1axUpV-0000qJ-Bu for guix-devel@gnu.org; Tue, 03 May 2016 03:33:20 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1axUpJ-0003rR-6k for guix-devel@gnu.org; Tue, 03 May 2016 03:33:07 -0400 Received: from mail-ig0-x22a.google.com ([2607:f8b0:4001:c05::22a]:37261) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1axUpH-0003dt-SZ for guix-devel@gnu.org; Tue, 03 May 2016 03:33:01 -0400 Received: by mail-ig0-x22a.google.com with SMTP id s8so12872970ign.0 for ; Tue, 03 May 2016 00:32:45 -0700 (PDT) In-Reply-To: List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: "Guix-devel" To: Ricardo Wurmus Cc: guix-devel@gnu.org --089e01538ac84cd6d30531eb1da6 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable 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 wrote: > > Hi Rob, > > > A guix-friendly licensed variant caller. > > > > From 78fb1be26ca1a0ac768ce5b98f7fd9f467870b84 Mon Sep 17 00:00:00 2001 > > From: Rob Syme > > 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=E2=80=99t 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 > --089e01538ac84cd6d30531eb1da6 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Ricardo

I'm sorry for not checki= ng the list beforehand! Interestingly, we ended up with very different solu= tions to the problem of including the freebayes dependencies. Using the rec= ursive git fetch compiles without issue for me and *seems* to produce sensi= ble results. Perhaps some non-guix packages are bleeding in from my configu= ration? 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 s= ubmodule problem, as we wouldn't need to update the hashes and urls for= =C2=A0bamtools-src,=C2=A0vcflib-src,=C2=A0tabixpp-src, etc.

=
On Mon, 2 May 2016 at 23:21 Ric= ardo Wurmus <ricardo.wur= mus@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!=C2=A0 I see that freebayes has a couple of git
submodules, e.g. for bamtools, intervaltree, and vcflib.=C2=A0 I remember Roel was working on this before, trying to untangle all the
dependencies.

See this discussion here:

=C2=A0 =C2=A0 http://lists.gnu.org= /archive/html/guix-devel/2016-03/msg00333.html

I don=E2=80=99t see any special treatment of these dependencies in your
package.=C2=A0 Is this not needed?=C2=A0 Or does the git checkout include a= ll the
bundled dependencies?

I think we should use one of the release tarballs instead and make sure
to package the dependencies separately.=C2=A0 Maybe you can cooperate with<= br> Roel, who has made a lot of progress on this end already.

What do you think?

~~ Ricardo
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