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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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/BSseeker2-v2.1.8.tar.gz"
version('2.1.8', sha256='34ebedce36a0fca9e22405d4c2c20bc978439d4a34d1d543657fbc53ff847934')
version('2.1.5', sha256='ac90fb4ad8853ee920f1ffea2b1a8cfffcdb1508ff34be0091d5a9c90ac8c74a',
url='https://github.com/BSSeeker/BSseeker2/archive/v2.1.7.tar.gz')
version('2.1.2', '5f7f0ef4071711e56b59c5c16b7f34a7',
url='https://github.com/BSSeeker/BSseeker2/archive/v2.1.2.tar.gz')
depends_on('python@2.6:', 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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