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| -rw-r--r-- | var/spack/repos/builtin/packages/rmats/package.py | 51 |
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')) |