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# Copyright 2013-2018 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 Soapindel(MakefilePackage):
"""SOAPindel is focusing on calling indels from the next-generation
paired-end sequencing data."""
homepage = "http://soap.genomics.org.cn/soapindel.html"
version('2.1.7.17', '317ef494173969cdc6a8244dd87d06bd',
url='http://soap.genomics.org.cn/down/SOAPindel_20130918_2.1.7.17.zip')
depends_on('perl', type=('build', 'run'))
build_directory = 'indel_detection.release'
def install(self, spec, prefix):
with working_dir('indel_detection.release'):
install_tree('tools', prefix.tools)
mkdirp(prefix.lib)
install('affine_align.pm', prefix.lib)
install('indel_lib.pm', prefix.lib)
mkdirp(prefix.bin)
install('assemble_align', prefix.bin)
install('cluster_reads', prefix.bin)
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('PERL5LIB', self.prefix.lib)
run_env.prepend_path('PATH', self.prefix.tools)
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