From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: Re: [PATCH] Add vcflib. Date: Wed, 20 Apr 2016 15:06:09 +0200 Message-ID: References: <878u1aa62m.fsf@gnu.org> 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]:33032) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1asrpk-00027z-S1 for guix-devel@gnu.org; Wed, 20 Apr 2016 09:06:21 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1asrpg-0007kh-DM for guix-devel@gnu.org; Wed, 20 Apr 2016 09:06:20 -0400 In-Reply-To: <878u1aa62m.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" To: Roel Janssen Cc: guix-devel@gnu.org Roel Janssen writes: > From c934cee6c84a39de36ecb4c3a85340ff025b1343 Mon Sep 17 00:00:00 2001 > From: Roel Janssen > Date: Tue, 22 Mar 2016 15:50:12 +0100 > Subject: [PATCH 6/8] gnu: Add fastahack. > * gnu/packages/bioinformatics.scm (fastahack): New variable. > --- > gnu/packages/bioinformatics.scm | 34 +++++++++++++++++++++++++++++++++= + > 1 file changed, 34 insertions(+) > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformat= ics.scm > index 261660f..9cbde46 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -4951,3 +4951,37 @@ combinatorial configurations.\" G Ehrlich - Jour= nal of the ACM (JACM), > (description "A program to compare version strings. It intends = to be a > replacement for strverscmp.") > (license license:gpl3+)))) > + > +(define-public fastahack > + (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd")) > + (package > + (name "fastahack") > + (version (string-append "0-1." (string-take commit 7))) > + (source (origin > + (method url-fetch) > + (uri (string-append "https://github.com/ekg/fastahack/archive/= " > + commit ".tar.gz")) > + (file-name (string-append name "-" version > "-checkout.tar.gz")) I don=E2=80=99t think we should add =E2=80=9Ccheckout=E2=80=9D here. > + (sha256 > + (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2= ")))) > + (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") "/b= in"))) > + (install-file "fastahack" bin))))))) > + (home-page "https://github.com/ekg/fastahack") > + (synopsis "Program for indexing and sequence extraction from > FASTA files") This sounds a bit off. It=E2=80=99s =E2=80=9Cindexing of ... FASTA files= =E2=80=9D (not =E2=80=9Cfrom=E2=80=9D) but =E2=80=9Csequence extraction from FASTA files=E2=80=9D. Maybe droppi= ng =E2=80=9CProgram for=E2=80=9D would help here: =E2=80=9CIndex and extract sequences from FASTA files=E2=80=9D What do you think? > + (description "Fastahack is a small application for indexing and = extracting > +sequences and subsequences from FASTA files. The included Fasta.cpp l= ibrary > +provides a FASTA reader and indexer that can be embeddedinto applicati= ons which > +would benefit from directly reading subsequences from FASTA files. Th= e library > +automatically handles index file generation and use.") =E2=80=9Cembeddedinto=E2=80=9D should be split. I would drop mention of =E2=80=9CFasta.cpp=E2=80=9D =E2=80=93 or is this = really the name of the library? > + ;; libdisorder is licensed GPLv2. The parent project (vcflib), = of which > + ;; this program is a submodule, is licensed MIT, which is the sa= me as > + ;; the Expat license. > + (license (list license:gpl2 license:expat))))) As before we use the license of this code and ignore the parent project=E2=80=99s license. Here=E2=80=99s a license problem, though. The files =E2=80=9CFasta.h=E2=80= =9D and =E2=80=9CFasta.cpp=E2=80=9D contain notices like this: > // ********************************************************************= ******* > // FastaIndex.h (c) 2010 Erik Garrison > // Marth Lab, Department of Biology, Boston College > // All rights reserved. > // --------------------------------------------------------------------= ------- > // Last modified: 5 February 2010 (EG) > // --------------------------------------------------------------------= ------- =E2=80=9Cdisorder.c=E2=80=9D has license GPLv2+. There=E2=80=99s a bug report mentioning this problem here: https://github.com/ekg/fastahack/issues/8 As it is now we cannot include this in Guix upstream unless the non-free files are removed in a snippet. ~~ Ricardo