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rmats: new package starting at 4.0.2 (#9243)

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* new package starting at 4.0.2
This commit is contained in:
Justin Stanley 2018-09-14 16:54:26 -05:00 committed by Todd Gamblin
parent 716ed92e32
commit dda27fc0d1
1 changed files with 51 additions and 0 deletions
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var/spack/repos/builtin/packages/rmats/package.py Normal file
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##############################################################################
# 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'))