rmats: new package starting at 4.0.2 (#9243)

* new package starting at 4.0.2

1 files changed, 51 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/rmats/package.py b/var/spack/repos/builtin/packages/rmats/package.py
new file mode 100644
index 0000000000..3f969b4b1c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/rmats/package.py
@@ -0,0 +1,51 @@
+##############################################################################
+# Copyright (c) 2013-2018, 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/spack/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 *
+from os import symlink
+
+
+class Rmats(Package):
+    """MATS is a computational tool to detect differential alternative
+       splicing events from RNA-Seq data."""
+
+    homepage = "https://rnaseq-mats.sourceforge.net/index.html"
+    url      = "https://downloads.sourceforge.net/project/rnaseq-mats/MATS/rMATS.4.0.2.tgz"
+
+    version('4.0.2', sha256='afab002a9ae836d396909aede96318f6dab6e5818078246419dd563624bf26d1')
+
+    depends_on('python@2.7:', type='run')
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('openblas')
+
+    def install(self, spec, prefix):
+        # since the tool is a python script we install it to /usr/lib
+        install_tree('rMATS-turbo-Linux-UCS4', join_path(prefix.lib, 'rmats'))
+
+        # the script has an appropriate shebang so a quick symlink will do
+        set_executable(join_path(prefix.lib, 'rmats/rmats.py'))
+        mkdirp(prefix.bin)
+        symlink(join_path(prefix.lib, 'rmats/rmats.py'),
+                join_path(prefix.bin, 'rmats'))