[PATCH] gnu: Add genometools.

[Justus Winter <justus@gnupg.org>]

* gnu-system.am (dist_patch_DATA): Add new patch.
* gnu/packages/bioinformatics.scm (genometools): New package.
* gnu/packages/patches/genometools-fix-testsuite.patch: New file.
---
 gnu-system.am                                      |  1 +
 gnu/packages/bioinformatics.scm                    | 40 ++++++++++++++++++++++
 .../patches/genometools-fix-testsuite.patch        | 18 ++++++++++
 3 files changed, 59 insertions(+)
 create mode 100644 gnu/packages/patches/genometools-fix-testsuite.patch

diff --git a/gnu-system.am b/gnu-system.am
index fd9795e..a03d4a5 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -479,6 +479,7 @@ dist_patch_DATA =						\
   gnu/packages/patches/gcc-cross-environment-variables.patch	\
   gnu/packages/patches/gcc-libvtv-runpath.patch			\
   gnu/packages/patches/gcc-5.0-libvtv-runpath.patch		\
+  gnu/packages/patches/genometools-fix-testsuite.patch		\
   gnu/packages/patches/geoclue-config.patch			\
   gnu/packages/patches/ghostscript-CVE-2015-3228.patch		\
   gnu/packages/patches/ghostscript-runpath.patch		\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 74761c0..11c39f5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -42,6 +42,8 @@
   #:use-module (gnu packages file)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages glib)
+  #:use-module (gnu packages gtk)
   #:use-module (gnu packages java)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages machine-learning)
@@ -1610,6 +1612,44 @@ the sequence of each record but can also be told to look in the header,
 comment or quality sections.")
       (license license:expat))))
 
+(define-public genometools
+  (package
+   (name "genometools")
+   (version "1.5.8")
+   (source (origin
+            (method url-fetch)
+            (uri (string-append "http://genometools.org/pub/genometools-"
+                                version
+                                ".tar.gz"))
+            (sha256
+             (base32
+              "1sq60y8blnl19229siprhz9dv5jzk42v0ihalncrdb1vvzklr1n1"))
+            (patches (list
+                      ;; This patch is already merged upstream, so it
+                      ;; can be dropped with the next release.
+                      (search-patch "genometools-fix-testsuite.patch")))))
+   (build-system gnu-build-system)
+   (arguments
+    '(#:make-flags (list "CC=gcc"
+                         (string-append "prefix="
+                                        (assoc-ref %outputs "out")))
+                   #:test-target "test"
+                   #:phases (alist-delete 'configure %standard-phases)))
+   (inputs `(("ruby" ,ruby)
+             ("python-2" ,python-2)
+             ("cairo" ,cairo)
+             ("pango" ,pango)
+             ("glib" ,glib)))
+   (native-inputs `(("pkg-config" ,pkg-config)))
+   (synopsis "Versatile open source genome analysis software")
+   (description
+    "The GenomeTools genome analysis system is a free collection of
+bioinformatics tools (in the realm of genome informatics) combined
+into a single binary named gt.  It is based on a C library named
+'libgenometools' which consists of several modules.")
+   (home-page "http://www.genometools.org/")
+   (license license:isc)))
+
 (define-public grit
   (package
     (name "grit")
diff --git a/gnu/packages/patches/genometools-fix-testsuite.patch b/gnu/packages/patches/genometools-fix-testsuite.patch
new file mode 100644
index 0000000..e898900
--- /dev/null
+++ b/gnu/packages/patches/genometools-fix-testsuite.patch
@@ -0,0 +1,18 @@
+diff --git a/testsuite/testsuite.rb b/testsuite/testsuite.rb
+index fcda4a8..f5e3906 100755
+--- a/testsuite/testsuite.rb
++++ b/testsuite/testsuite.rb
+@@ -127,9 +127,10 @@ def with_environment(variables={})
+ end
+ 
+ def python_tests_runnable?
+-  if `which python`.empty? then
+-    return false
+-  end
++  return false unless
++    ENV['PATH'].split(File::PATH_SEPARATOR).any? do |directory|
++      File.executable?(File.join(directory, "python"))
++    end
+   require "open3"
+   runline = "python #{$gtpython}/gt/dlload.py"
+   with_environment({"PYTHONPATH" => $gtpython, \
-- 
2.1.4