cufflinks: new package (#5158)

1 files changed, 46 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/cufflinks/package.py b/var/spack/repos/builtin/packages/cufflinks/package.py
new file mode 100644
index 0000000000..c0d331439b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/cufflinks/package.py
@@ -0,0 +1,46 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class Cufflinks(Package):
+    """Cufflinks assembles transcripts, estimates their abundances, and tests
+       for differential expression and regulation in RNA-Seq samples."""
+
+    homepage = "http://cole-trapnell-lab.github.io/cufflinks"
+    url      = "http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz"
+
+    version('2.2.1', '7e693d182dcfda8aeef8523219ea9ea7')
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        install('cuffcompare', prefix.bin)
+        install('cuffdiff', prefix.bin)
+        install('cufflinks', prefix.bin)
+        install('cuffmerge', prefix.bin)
+        install('cuffnorm', prefix.bin)
+        install('cuffquant', prefix.bin)
+        install('gffread', prefix.bin)
+        install('gtf_to_sam', prefix.bin)