[PATCH] gnu: Add ruby-libxml and bioruby.

[Pjotr Prins <pjotr.public12@thebird.nl>]

    * gnu/packages/ruby.scm (ruby-libxml): New variable.
    * gnu/packages/bioinformatics.scm (bioruby): New variable.
---
 gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++++++++++++++++++++++
 gnu/packages/ruby.scm           | 26 +++++++++++++++++++++++
 2 files changed, 73 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1f34211..b297ef2 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)
+    (native-inputs `(("ruby-libxml" ,ruby-libxml)))
+    (inputs
+     `(("coreutils" ,coreutils)  ; required for /bin/echo in tests
+       ("which" ,which)))        ; required for tests
+    (arguments
+     `(#:phases
+        (alist-cons-before
+         'build 'replace-sh-commands
+         (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"))))
+         %standard-phases)))
+    (synopsis
+      "Ruby library, shell and utilities for bioinformatics")
+    (description
+      "BioRuby comes with a comprehensive set of free 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+), scripts in samples (GPL2 and GPL2+)
+    (license (list license:ruby license:lgpl2.1+ license:gpl2
+                   license:gpl2+ ))))
diff --git a/gnu/packages/ruby.scm b/gnu/packages/ruby.scm
index ee0acc8..1ca5f96 100644
--- a/gnu/packages/ruby.scm
+++ b/gnu/packages/ruby.scm
@@ -465,6 +465,32 @@ extensions.")
     (home-page "http://codeforpeople.com/lib/ruby/orderedhash/")
     (license license:public-domain)))
 
+(define-public ruby-libxml
+  (package
+    (name "ruby-libxml")
+    (version "2.8.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (rubygems-uri "libxml-ruby" version))
+        (sha256
+          (base32
+            "1dhjqp4r9vkdp00l6h1cj8qfndzxlhlxk6b9g0w4v55gz857ilhb"))))
+    (build-system ruby-build-system)
+    (inputs `(("zlib" ,zlib)
+              ("libxml2" ,libxml2)))
+    (arguments
+     '(#:tests? #f  ; tests need installation of build first
+       #:gem-flags (list "--"
+                         (string-append "--with-xml2-include="
+                                        (assoc-ref %build-inputs "libxml2")
+                                        "/include/libxml2" ))))
+    (synopsis "Ruby bindings for the GNOME Libxml2 XML toolkit")
+    (description "The Libxml-Ruby project provides Ruby language
+bindings for the GNOME Libxml2 XML toolkit.")
+    (home-page "http://xml4r.github.com/libxml-ruby")
+    (license license:expat)))
+
 (define-public ruby-xml-simple
   (package
     (name "ruby-xml-simple")
-- 
2.4.3