From mboxrd@z Thu Jan 1 00:00:00 1970 From: Roel Janssen Subject: Re: [PATCH] gnu: Add freebayes. Date: Thu, 10 Mar 2016 10:56:38 +0100 Message-ID: <87r3fi64h5.fsf@gnu.org> References: <874mchc6uz.fsf@gnu.org> <20160309065320.GB16207@thebird.nl> <20160309073158.GA24805@jasmine> Mime-Version: 1.0 Content-Type: text/plain Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:59810) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1adxKd-0007eg-TF for guix-devel@gnu.org; Thu, 10 Mar 2016 04:56:36 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1adxKa-00078J-KG for guix-devel@gnu.org; Thu, 10 Mar 2016 04:56:35 -0500 In-reply-to: <20160309073158.GA24805@jasmine> 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: Leo Famulari Cc: guix-devel@gnu.org Leo Famulari writes: > On Wed, Mar 09, 2016 at 07:53:20AM +0100, Pjotr Prins wrote: >> On Tue, Mar 08, 2016 at 04:44:13PM +0100, Roel Janssen wrote: >> > 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). >> >> This approach is very common in bioinformatics and one way they fight >> dependency hell. Not the best way, admittedly. >> >> It may be worthwhile to package vcflib, for example, separately as >> freebayes merely requires the header files to compile. The problem is >> that that te current vcflib does not include the headers from a >> default install, if I understand Roel correctly. Ricardo, can you >> advice on this? Should we add the headers in guix through a vcflib >> installer? I would like to propose the following: - Separate the packages, and when needed, add specific versions of the packages. Instead of trying to package arbitrary Git commits, I will look into whether I can use release versions instead, without impacting the final FreeBayes binary. - Use ,(package-source ...) to unpack the sources of the packages to satisfy the "submodules" structure of projects that use this. This way we can separate the packages, which yields the programs that are now hidden in submodule sources. It also gives us more complete package descriptions for them. We don't have to heavily modify the project setups that rely on submodules (just extract sources the way we do now). I am working on doing this for FreeBayes. It should yield separate packages for: vcflib, tabixpp, multichoose, smithwaterman, filevercmp and fsom. I want to find out whether I can make "intervaltree" a library, as it is meant to be: https://github.com/ekg/intervaltree WDYT? Kind regards, Roel Janssen