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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 Bsseeker2(Package):
"""A versatile aligning pipeline for bisulfite sequencing data."""
homepage = "http://pellegrini.mcdb.ucla.edu/BS_Seeker2"
url = "https://github.com/BSSeeker/BSseeker2/archive/v2.1.2.tar.gz"
version('2.1.2', '5f7f0ef4071711e56b59c5c16b7f34a7')
depends_on('python@2.6:2.999', type=('build', 'run'))
depends_on('py-pysam', type=('build', 'run'))
def install(self, spec, prefix):
mkdirp(prefix.bin)
install('Antisense.py', prefix.bin)
install_tree('bs_index', prefix.bin.bs_index)
install('bs_seeker2-build.py', prefix.bin)
install_tree('bs_utils', prefix.bin.bs_utils)
install_tree('galaxy', prefix.bin.galaxy)
install_tree('bs_align', prefix.bin.bs_align)
install('bs_seeker2-align.py', prefix.bin)
install('bs_seeker2-call_methylation.py', prefix.bin)
install('FilterReads.py', prefix.bin)
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