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Features/py breakseq2 (#7642)

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* added htslib 1.7 and checksum

* py-breakseq2: new package!!!!

* py-breakseq2: fixed whitespace

* py-breakseq2: added additional dependencies

* py-breakseq2: fixed build/run  depends

* py-breakseq2: added additonal dependencies
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David Orman 2018-03-31 10:24:16 -05:00 committed by Adam J. Stewart
parent 42c14e0fdb
commit c032b2d9db
1 changed files with 41 additions and 0 deletions
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var/spack/repos/builtin/packages/py-breakseq2/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 PyBreakseq2(PythonPackage):
"""nucleotide-resolution analysis of structural variants"""
homepage = "http://bioinform.github.io/breakseq2/"
url = "https://github.com/bioinform/breakseq2/archive/2.2.tar.gz"
version('2.2', '6fd5a103c2781717b0b1d0efcbdc17e7')
depends_on('py-setuptools', type='build')
depends_on('py-biopython@1.65', type=('build', 'run'))
depends_on('py-cython', type='build')
depends_on('py-pysam@0.7.7', type=('build', 'run'))
depends_on('bwa', type='run')
depends_on('samtools', type='run')