From mboxrd@z Thu Jan 1 00:00:00 1970 From: Roel Janssen Subject: Re: [PATCH] Add vcflib. Date: Tue, 26 Apr 2016 23:50:29 +0200 Message-ID: <87bn4w11lm.fsf@gnu.org> References: <878u1aa62m.fsf@gnu.org> Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:45675) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1avAsX-0007LU-T9 for guix-devel@gnu.org; Tue, 26 Apr 2016 17:50:48 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1avAsU-0000WU-JB for guix-devel@gnu.org; Tue, 26 Apr 2016 17:50:45 -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: Ricardo Wurmus Cc: guix-devel@gnu.org Ricardo Wurmus writes: > Roel Janssen writes: > >> From e75aa388931c92657336c8a15f88b6a0273f5e02 Mon Sep 17 00:00:00 2001 >> From: Roel Janssen >> Date: Tue, 22 Mar 2016 15:01:37 +0100 >> Subject: [PATCH 2/8] gnu: Add smithwaterman. > >> * gnu/packages/bioinformatics.scm (smithwaterman): New variable. >> --- >> gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ >> 1 file changed, 31 insertions(+) > >> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm >> index 6792be9..fa7ba24 100644 >> --- a/gnu/packages/bioinformatics.scm >> +++ b/gnu/packages/bioinformatics.scm >> @@ -4830,3 +4830,34 @@ group or two ChIP groups run under different conditions.") >> (description "This is a C++ wrapper around the Tabix project which abstracts >> some of the details of opening and jumping in tabix-indexed files.") >> (license license:expat))) >> + >> +(define-public smithwaterman >> + (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) > > As there have been new commits since you posted this patch could you add > a comment that explains why it should be this particular commit? Is it > because this is the version of the submodule of vcflib? That is the reason. I will add a comment in the next patch I send. >> + (package >> + (name "smithwaterman") >> + (version (string-append "0-1." (string-take commit 7))) >> + (source (origin >> + (method url-fetch) >> + (uri (string-append "https://github.com/ekg/smithwaterman/archive/" >> + commit ".tar.gz")) >> + (file-name (string-append name "-" version "-checkout.tar.gz")) >> + (sha256 >> + (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b")))) >> + (build-system gnu-build-system) >> + (arguments >> + `(#:tests? #f ; There are no tests to run. >> + #:phases >> + (modify-phases %standard-phases >> + (delete 'configure) ; There is no configure phase. >> + (replace 'install >> + (lambda* (#:key outputs #:allow-other-keys) >> + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) >> + (install-file "smithwaterman" bin))))))) >> + (home-page "https://github.com/ekg/smithwaterman") >> + (synopsis "Implementation of the Smith-Waterman algorithm") >> + (description "This package provides an implementation of the Smith-Waterman >> +algorithm.") >> + ;; libdisorder is licensed GPLv2. The parent project (vcflib), of which >> + ;; this program is a submodule, is licensed MIT, which is the same as >> + ;; the Expat license. >> + (license (list license:gpl2 license:expat))))) > > As far as I can see the license is GPLv2+ as it doesn’t specifically > restricts users to version 2. > > The license of the parent project doesn’t matter in this case, so > “(license license:gpl2+)” would seem to be enough. Where can you see that it's GPLv2+? I haven't found any licensing information other than libdisorder. I contacted the author about this. I'm confident it's not an intentional nonfree program, but we will have to wait and see. Kind regards, Roel Janssen