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Create new package: fastgbs and its dependency platypus. (#8174)

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* pushing partially done recipe for fast-gbs and platypus

* modify platypus

* change header

* fast-gbs: change dependency type.

* modify dependency type.

* modify dependency type.

* fast-gbs: Change dependency type to run.
This commit is contained in:
lingnanyuan 2018-05-21 16:13:05 -05:00 committed by Adam J. Stewart
parent 2cfde03a60
commit 646771300d
2 changed files with 97 additions and 0 deletions
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var/spack/repos/builtin/packages/fast-gbs/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 *
class FastGbs(Package):
"""A bioinformatic pipeline designed to extract a high-quality SNP catalog
starting from FASTQ files obtained from sequencing
genotyping-by-sequencing (GBS) libraries."""
homepage = "https://bitbucket.org/jerlar73/fast-gbs"
url = "https://bitbucket.org/jerlar73/fast-gbs"
version('2017-01-25', git='https://bitbucket.org/jerlar73/fast-gbs.git', commit='3b3cbffa84d269419692067c6a3de08b3b88849c')
depends_on('parallel', type='run')
depends_on('python@2.7:', type='run')
depends_on('sabre', type='run')
depends_on('py-cutadapt', type='run')
depends_on('bwa', type='run')
depends_on('samtools', type='run')
depends_on('platypus', type='run')
depends_on('py-pyvcf', type='run')
def install(self, spec, prefix):
mkdirp(prefix.bin)
install('fastgbs.sh', prefix.bin)
install('parameters.txt', prefix.bin)
install('makeDir.sh', prefix.bin)
install('makeBarcodeSabre.py', prefix.bin)
install('vcf2txt.py', prefix.bin)
install('txt2unix.sh', prefix.bin)

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var/spack/repos/builtin/packages/platypus/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 *
class Platypus(Package):
"""A Haplotype-Based Variant Caller For Next Generation Sequence Data"""
homepage = "http://www.well.ox.ac.uk/platypus"
url = "http://www.well.ox.ac.uk/bioinformatics/Software/Platypus-latest.tgz"
version('0.8.1', 'edf3fb5bf080241ddb75a413c8529d57')
depends_on('python@2.6:', type=('build', 'run'))
depends_on('py-cython', type='build')
depends_on('htslib')
def install(self, spec, prefix):
buildPlatypus = Executable('./buildPlatypus.sh')
buildPlatypus()
install_tree('.', prefix.bin)