>From dd1fb03349d2ba2e7f36252d68f3de11f21b8866 Mon Sep 17 00:00:00 2001
Date: Thu, 17 Sep 2015 06:17:44 +0000
Subject: [PATCH] gnu: Add ruby-libxml and bioruby.
To: address@hidden
From: Pjotr Prins <address@hidden>

* gnu/packages/bioinformatics.scm (bioruby): New variable.
---
 gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1f34211..5df77a9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2642,3 +2642,50 @@ position for indels.  Bio-locus allows users to store this chr+pos or
 chr+pos+alt information in a database.")
     (home-page "https://github.com/pjotrp/bio-locus")
     (license license:expat)))
+
+(define-public bioruby
+  (package
+    (name "bioruby")
+    (version "1.5.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (rubygems-uri "bio" version))
+        (sha256
+          (base32
+           "01k2fyjl5fpx4zn8g6gqiqvsg2j1fgixrs9p03vzxckynxdq3wmc"))))
+    (build-system ruby-build-system)
+    (propagated-inputs `(("ruby-libxml" ,ruby-libxml)))
+    (native-inputs
+     `(("which" ,which)))  ; required for test phase
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-before
+          'build 'patch-test-command
+         (lambda _
+           (substitute* '("test/functional/bio/test_command.rb")
+             (("/bin/sh") (which "sh")))
+           (substitute* '("test/functional/bio/test_command.rb")
+             (("/bin/ls") (which "ls")))
+           (substitute* '("test/functional/bio/test_command.rb")
+             (("which") (which "which")))
+           (substitute* '("test/functional/bio/test_command.rb",
+                          "test/data/command/echoarg2.sh")
+             (("/bin/echo") (which "echo")))
+         #t)))))
+    (synopsis
+      "Ruby library, shell and utilities for bioinformatics")
+    (description
+      "BioRuby comes with a comprehensive set of development tools and
+libraries for bioinformatics and molecular biology, for the Ruby
+programming language.  BioRuby has components for sequence analysis,
+pathway analysis, protein modelling and phylogenetic analysis; it
+supports many widely used data formats and provides easy access to
+databases, external programs and public web services, including BLAST,
+KEGG, GenBank, MEDLINE and GO.")
+    (home-page "http://bioruby.org/")
+    ;; Code is released under Ruby license, except for setup
+    ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+)
+    (license (list license:ruby license:lgpl2.1+ license:gpl2
+                   license:gpl2+ ))))
-- 
2.4.3