From mboxrd@z Thu Jan 1 00:00:00 1970 From: Leo Famulari Subject: Re: [PATCH] gnu: Add freebayes. Date: Tue, 8 Mar 2016 18:55:15 -0500 Message-ID: <20160308235515.GC24107@jasmine> References: <874mchc6uz.fsf@gnu.org> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:55376) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1adRTF-0001Qe-8I for guix-devel@gnu.org; Tue, 08 Mar 2016 18:55:22 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1adRTC-0002CG-17 for guix-devel@gnu.org; Tue, 08 Mar 2016 18:55:21 -0500 Received: from out5-smtp.messagingengine.com ([66.111.4.29]:36052) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1adRTB-0002B5-HA for guix-devel@gnu.org; Tue, 08 Mar 2016 18:55:17 -0500 Content-Disposition: inline In-Reply-To: <874mchc6uz.fsf@gnu.org> 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-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: Roel Janssen Cc: guix-devel@gnu.org On Tue, Mar 08, 2016 at 04:44:13PM +0100, Roel Janssen wrote: Thanks for the patch! This looks like a big one! [...] > + (native-inputs > + `(("cmake" ,cmake) > + ("htslib" ,htslib) > + ("zlib" ,zlib) > + ("python" ,python-2) > + ("perl" ,perl) > + ("bamtools-src" > + ,(origin > + (method url-fetch) > + (uri (string-append "https://github.com/ekg/bamtools/archive/" > + "e77a43f5097ea7eee432ee765049c6b246d49baa" ".tar.gz")) > + (file-name "bamtools-src.tar.gz") > + (sha256 > + (base32 "0rqymka21g6lfjfgxzr40pxz4c4fcl77jpy1np1li70pnc7h2cs1")))) [... more sub-modules ...] > + (arguments > + `(#:tests? #f Can you say why tests are disabled? It can be as simple as "no test suite". > + #:phases > + (modify-phases %standard-phases > + (delete 'configure) > + (delete 'check) This can be removed when using "#:tests? #f", which is the preferred way to skip tests. [...] > Dear Guix, > > I have a patch to add another bioinformatics tool: FreeBayes. It is a > rather long patch, so suspect it isn't completely 'guix-proof'. > > 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). You can specify the version of dependencies when you list them in your package. There is an example of this in the package definition of fltk [0]. Is that not an appropriate solution for freebayes? In any case, I think we should find some way to specify the license of the code in all those modules. I think somebody with some more experience should weigh in... Cc-ing Ricardo since he also packages a lot of bioinformatics packages. Thanks again for putting such a complicated patch together! We will find the best way to add freebayes to the distribution :) [0] Due to a recent change, the most correct method of specifying the version uses '@' to separate the package name and version rather than '-'.