From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] gnu: Add freebayes Date: Mon, 2 May 2016 17:21:29 +0200 Message-ID: References: Mime-Version: 1.0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:48009) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1axFff-0008Ln-Gv for guix-devel@gnu.org; Mon, 02 May 2016 11:22:09 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1axFfT-0005rv-QZ for guix-devel@gnu.org; Mon, 02 May 2016 11:21:58 -0400 Received: from sinope02.bbbm.mdc-berlin.de ([141.80.25.24]:47545) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1axFfS-0005m4-IA for guix-devel@gnu.org; Mon, 02 May 2016 11:21:51 -0400 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: Rob Syme Cc: guix-devel@gnu.org 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