From mboxrd@z Thu Jan 1 00:00:00 1970 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) Subject: Re: [PATCH] gnu: Add TopHat. Date: Fri, 22 Jan 2016 18:09:57 +0100 Message-ID: <87mvrx4k2i.fsf@gnu.org> 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]:39243) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aMfDn-0003wx-Mu for guix-devel@gnu.org; Fri, 22 Jan 2016 12:10:04 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aMfDj-0000XC-Lx for guix-devel@gnu.org; Fri, 22 Jan 2016 12:10:03 -0500 In-Reply-To: (Ricardo Wurmus's message of "Tue, 19 Jan 2016 14:52:48 +0100") 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: Ricardo Wurmus Cc: guix-devel Ricardo Wurmus skribis: > I=E2=80=99m happy to be able to submit a patch to add TopHat. It=E2=80= =99s a very > popular piece of bioinformatics software that I didn=E2=80=99t submit to = Guix > upstream before as the license wasn=E2=80=99t clear. The latest release = at that > time contained a LICENSE file with the text of the Artistic license 1.0. > > The new 2.1.0 release no longer contains this file; instead it declares > the license to be the Boost Software license 1.0. Additionally, the > license has been clarified on a Github issue (which I linked to). I > only just noticed this because a user asked me to package the latest > version and I was very happy to see the Artistic license removed. One more free software package, this is good news! > The sources of TopHat bundle the SeqAn header library (version 1.3) and > the sources of samtools 0.1.18. I=E2=80=99m patching the Makefile in a b= uild > phase to use our packages for seqan@1.4.2 and samtools@0.1.19. A > snippet removes the bundled sources. Good. > From 91f7bacd8657b4be6669a2e72a2ca74b2e44a62f Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus > Date: Tue, 19 Jan 2016 14:29:19 +0100 > Subject: [PATCH] gnu: Add TopHat. > > * gnu/packages/bioinformatics.scm (tophat): New variable. > * gnu/packages/patches/tophat-build-with-later-seqan.patch: New file. > * gnu-system.am (dist_patch_DATA): Add it. [...] > + (synopsis "Spliced read mapper for RNA-Seq") > + (description > + "TopHat is a fast splice junction mapper for RNA-Seq reads. It ali= gns It would be nice to contextualize a bit, for instance by adding a word after =E2=80=9CRNA-Seq=E2=80=9D, like: =E2=80=A6 for RNA-Seq bioinformatics foobars or: =E2=80=A6 for the RNA-Seq bioinformatics thingie Something like that. :-) > + ;; TopHat is released under the Boost Software License, Version 1.0 > + ;; See https://github.com/infphilo/tophat/issues/11#issuecomment-121= 589893 > + (license (license:x11-style "http://www.boost.org/LICENSE_1_0.txt" > + "Some components have other similar lice= nces.")))) You can use =E2=80=98license:boost1.0=E2=80=99 here. Otherwise LGTM, thanks! Ludo=E2=80=99.