From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ricardo Wurmus Subject: [PATCH] Add (minimal) BioPerl. Date: Wed, 3 Jun 2015 17:53:14 +0200 Message-ID: Mime-Version: 1.0 Content-Type: text/x-patch Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:55612) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z0Ayu-0005DK-4b for guix-devel@gnu.org; Wed, 03 Jun 2015 11:53:29 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z0Ayn-00045F-VA for guix-devel@gnu.org; Wed, 03 Jun 2015 11:53:28 -0400 Received: from pegasus.bbbm.mdc-berlin.de ([141.80.25.20]:45464) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z0Ayn-00044e-Hw for guix-devel@gnu.org; Wed, 03 Jun 2015 11:53:21 -0400 Received: from localhost (localhost [127.0.0.1]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 3F2C2380C41 for ; Wed, 3 Jun 2015 17:53:19 +0200 (CEST) Received: from pegasus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (pegasus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id SMfspnZFE8n2 for ; Wed, 3 Jun 2015 17:53:13 +0200 (CEST) Received: from HTCAONE.mdc-berlin.net (mab.citx.mdc-berlin.de [141.80.36.102]) by pegasus.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Wed, 3 Jun 2015 17:53:13 +0200 (CEST) Content-Disposition: inline; filename="0001-gnu-Add-BioPerl.patch" 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: guix-devel >From e8cffdb9e7a2447657b3f700b2f0beb00ad0f98e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 3 Jun 2015 17:44:20 +0200 Subject: [PATCH] gnu: Add BioPerl. * gnu/packages/bioinformatics.scm (bioperl-minimal): New variable. --- gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index fd1c1dd..8d59768 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -225,6 +225,42 @@ pybedtools extends BEDTools by offering feature-level manipulations from with Python.") (license license:gpl2+))) +(define-public bioperl-minimal + (package + (name "bioperl-minimal") + (version "1.6.924") + (source + (origin + (method url-fetch) + (uri (string-append "mirror://cpan/authors/id/C/CJ/CJFIELDS/BioPerl-" + version ".tar.gz")) + (sha256 + (base32 + "1l3npcvvvwjlhkna9dndpfv1hklhrgva013kw96m0n1wpd37ask1")))) + (build-system perl-build-system) + (inputs + `(("perl-module-build" ,perl-module-build) + ("perl-data-stag" ,perl-data-stag) + ("perl-libwww" ,perl-libwww) + ("perl-uri" ,perl-uri))) + (native-inputs + `(("perl-test-most" ,perl-test-most))) + (native-search-paths (list (search-path-specification + (variable "PERL5LIB") + (files '("lib/perl5/site_perl"))))) + (home-page "http://search.cpan.org/dist/BioPerl") + (synopsis "Bioinformatics toolkit") + (description + "BioPerl is the product of a community effort to produce Perl code which +is useful in biology. Examples include Sequence objects, Alignment objects +and database searching objects. These objects not only do what they are +advertised to do in the documentation, but they also interact - Alignment +objects are made from the Sequence objects, Sequence objects have access to +Annotation and SeqFeature objects and databases, Blast objects can be +converted to Alignment objects, and so on. This means that the objects +provide a coordinated and extensible framework to do computational biology.") + (license (package-license perl)))) + (define-public python-biopython (package (name "python-biopython") -- 2.1.0