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hybpiper: new package (#4720)

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* hybpiper: new package and spades dependency

* hybpiper: making flkae8 happy

* hybpiper: fixing dependency errors

* fixing python dep type

* removing cmake from spade dependencies
This commit is contained in:
Audrey Thoma 2017-07-14 15:48:30 -05:00 committed by Adam J. Stewart
parent c78ee4a733
commit 1e205c09d8
2 changed files with 104 additions and 0 deletions
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var/spack/repos/builtin/packages/hybpiper/package.py Normal file
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##############################################################################
# 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 *
import glob
import os
class Hybpiper(Package):
"""HybPiper was designed for targeted sequence capture, in which DNA
sequencing libraries are enriched for gene regions of interest,
especially for phylogenetics. HybPiper is a suite of Python scripts
that wrap and connect bioinformatics tools in order to extract target
sequences from high-throughput DNA sequencing reads"""
homepage = "https://github.com/mossmatters/HybPiper"
url = "https://github.com/mossmatters/HybPiper/archive/v1.2.0.tar.gz"
version('1.2.0', '0ad78e9ca5e3f23ae0eb6236b07e1780')
depends_on('python@2.7:', type=('build', 'run'))
depends_on('py-biopython', type=('build', 'run'))
depends_on('exonerate')
depends_on('blast-plus')
depends_on('spades')
depends_on('parallel')
depends_on('bwa')
depends_on('samtools')
def setup_envionment(self, spack_env, run_env):
run_env.set('HYBPIPER_HOME', prefix)
def install(self, spec, prefix):
mkdirp(prefix.bin)
files = glob.iglob("*.py")
for file in files:
if os.path.isfile(file):
install(file, prefix.bin)

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var/spack/repos/builtin/packages/spades/package.py Normal file
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##############################################################################
# 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 Spades(CMakePackage):
"""SPAdes - St. Petersburg genome assembler - is intended for both
standard isolates and single-cell MDA bacteria assemblies."""
homepage = "http://cab.spbu.ru/software/spades/"
url = "http://cab.spbu.ru/files/release3.10.1/SPAdes-3.10.1.tar.gz"
version('3.10.1', 'dcab7d145af81b59cc867562f27536c3')
depends_on('python', type=('build', 'run'))
depends_on('zlib')
depends_on('bzip2')
conflicts('%gcc@7.1.0:')
@property
def root_cmakelists_dir(self):
return join_path(self.stage.source_path, 'src')