From mboxrd@z Thu Jan 1 00:00:00 1970 From: Justus Winter Subject: [PATCH] gnu: Add genometools. Date: Sun, 14 Feb 2016 15:56:22 +0100 Message-ID: <1455461782-24162-2-git-send-email-justus@gnupg.org> References: <1455461782-24162-1-git-send-email-justus@gnupg.org> Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:34402) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aUy6N-0006ZB-5G for guix-devel@gnu.org; Sun, 14 Feb 2016 09:56:44 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1aUy6I-0006Wd-4g for guix-devel@gnu.org; Sun, 14 Feb 2016 09:56:43 -0500 Received: from cryptobitch.de ([88.198.7.68]:60902 helo=mail.cryptobitch.de) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1aUy6H-0006WU-S3 for guix-devel@gnu.org; Sun, 14 Feb 2016 09:56:38 -0500 Received: from mail.jade-hamburg.de (unknown [85.183.43.52]) (using TLSv1 with cipher DHE-RSA-AES256-SHA (256/256 bits)) (No client certificate requested) by mail.cryptobitch.de (Postfix) with ESMTPSA id 75E82999333 for ; Sun, 14 Feb 2016 15:56:35 +0100 (CET) In-Reply-To: <1455461782-24162-1-git-send-email-justus@gnupg.org> List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: guix-devel@gnu.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