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phantompeakqualtools: new package (#6403)

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Audrey Thoma 2017-11-21 16:58:20 -06:00 committed by Christoph Junghans
parent 9e013ee036
commit a0df5ae3e0
2 changed files with 93 additions and 0 deletions
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var/spack/repos/builtin/packages/phantompeakqualtools/package.py Normal file
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##############################################################################
# Copyright (c) 2013-2017, 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 *
class Phantompeakqualtools(RPackage):
"""This package computes informative enrichment and quality measures for
ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data."""
homepage = "https://github.com/kundajelab/phantompeakqualtools"
url = "https://github.com/kundajelab/phantompeakqualtools/archive/1.2.tar.gz"
version('1.2', 'e94943a42132b9ff2886f006ab34c121')
depends_on('awk')
depends_on('samtools')
depends_on('r', type=('build', 'run'))
depends_on('r-phantompeakqualtools', type=('build', 'run'))
def install(self, spec, prefix):
mkdirp(prefix.bin)
install('run_spp.R', prefix.bin)

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var/spack/repos/builtin/packages/r-phantompeakqualtools/package.py Normal file
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##############################################################################
# Copyright (c) 2013-2017, 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 *
class RPhantompeakqualtools(RPackage):
"""Computes informative enrichment and quality measures for
ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. This is a modified version
of r-spp to be used in conjunction with the phantompeakqualtools
package."""
homepage = "https://github.com/kundajelab/phantompeakqualtools"
url = "https://github.com/kundajelab/phantompeakqualtools/raw/master/spp_1.14.tar.gz"
version('1.14', '4de207d570999170c1bf45bcba8c6d2d')
depends_on('boost@1.41.0:')
depends_on('r-catools', type=('build', 'run'))
depends_on('r-snow', type=('build', 'run'))
depends_on('r-snowfall', type=('build', 'run'))
depends_on('r-bitops', type=('build', 'run'))
depends_on('r-rsamtools', type=('build', 'run'))
conflicts('%gcc@6:')
def setup_environment(self, spack_env, run_env):
spack_env.set('BOOST_ROOT', self.spec['boost'].prefix)