From a7f69eb16e91ca94e5894b234a98a7f14e78fd64 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 | 50 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index fc03062..5ea0609 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -226,6 +226,56 @@ 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)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after
+          'install 'wrap-programs
+          (lambda* (#:key outputs #:allow-other-keys)
+            ;; Make sure all executables in "bin" find the required Perl
+            ;; modules at runtime.
+            (let* ((out (assoc-ref outputs "out"))
+                   (bin (string-append out "/bin/"))
+                   (path (string-append out "/lib/perl5/site_perl:"
+                                        (getenv "PERL5LIB"))))
+              (for-each (lambda (file)
+                          (wrap-program file
+                            `("PERL5LIB" ":" prefix (,path))))
+                        (find-files bin "\\.pl$"))
+              #t))))))
+    (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)))
+    (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