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[PATCH] gnu: Add genometools.
From: |
Justus Winter |
Subject: |
[PATCH] gnu: Add genometools. |
Date: |
Sun, 14 Feb 2016 15:56:22 +0100 |
* 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
- New package 'genometools', Justus Winter, 2016/02/14
- [PATCH] gnu: Add genometools.,
Justus Winter <=
- Re: [PATCH] gnu: Add genometools., Andreas Enge, 2016/02/14
- [PATCH] gnu: Add genometools., Justus Winter, 2016/02/14
- Message not available
- Re: [PATCH] gnu: Add genometools., Ben Woodcroft, 2016/02/14
- Re: [PATCH] gnu: Add genometools., Justus Winter, 2016/02/15
- Re: [PATCH] gnu: Add genometools., Ricardo Wurmus, 2016/02/15
Re: [PATCH] gnu: Add genometools., Andreas Enge, 2016/02/14