From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: guix-devel <guix-devel@gnu.org>
Subject: [PATCH] Add (minimal) BioPerl.
Date: Wed, 3 Jun 2015 17:53:14 +0200 [thread overview]
Message-ID: <idj6174g55h.fsf@bimsb-sys02.mdc-berlin.net> (raw)
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From e8cffdb9e7a2447657b3f700b2f0beb00ad0f98e Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
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
next reply other threads:[~2015-06-03 15:53 UTC|newest]
Thread overview: 13+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-06-03 15:53 Ricardo Wurmus [this message]
2015-06-03 16:00 ` [PATCH] Add (minimal) BioPerl Andreas Enge
2015-06-04 16:19 ` Ludovic Courtès
2015-06-04 21:37 ` Pjotr Prins
2015-06-06 17:48 ` Ludovic Courtès
2015-06-06 17:52 ` Ricardo Wurmus
2015-06-06 18:05 ` Ludovic Courtès
2015-06-17 13:24 ` Ricardo Wurmus
2015-06-21 21:04 ` Ludovic Courtès
2015-07-21 8:41 ` Ricardo Wurmus
2015-07-21 9:24 ` Eric Bavier
2015-08-24 13:03 ` Ricardo Wurmus
2015-08-25 21:44 ` Ludovic Courtès
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