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# Copyright 2013-2022 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 Cnvnator(MakefilePackage):
"""A tool for CNV discovery and genotyping
from depth-of-coverage by mapped reads."""
homepage = "https://github.com/abyzovlab/CNVnator"
url = "https://github.com/abyzovlab/CNVnator/archive/v0.3.3.tar.gz"
version('0.3.3', sha256='58c5acf61f9a1e5febf546c196f8917a5e084b729e5c4cfd3eba83471b3fe5c1')
depends_on('samtools@:1.13')
depends_on('htslib')
depends_on('root')
depends_on('bzip2')
depends_on('curl')
depends_on('xz')
depends_on('zlib')
depends_on('libdeflate')
depends_on('openssl')
def edit(self, spec, prefix):
makefile = FileFilter('Makefile')
# Replace -fopenmp with self.compiler.openmp_flag
makefile.filter('-fopenmp', self.compiler.openmp_flag)
# Replace CXX with CXXFLAGS
makefile.filter('CXX.*=.*',
r'CXXFLAGS = -DCNVNATOR_VERSION=\"$(VERSION)\"'
' $(OMPFLAGS)'
' {0}'.format(self.compiler.cxx11_flag))
makefile.filter('$(CXX)', '$(CXX) $(CXXFLAGS)', string=True)
# Replace -I$(SAMDIR) with -I$(SAMINC)
makefile.filter('-I$(SAMDIR)', '-I$(SAMINC)', string=True)
# Link more libs
ldflags = [
spec['zlib'].libs.ld_flags,
spec['bzip2'].libs.ld_flags,
spec['curl'].libs.ld_flags,
spec['xz'].libs.ld_flags,
spec['libdeflate'].libs.ld_flags,
spec['openssl'].libs.ld_flags,
]
makefile.filter('^override LIBS.*',
'override LIBS += {0}'.format(' '.join(ldflags)))
def build(self, spec, prefix):
make('ROOTSYS={0}'.format(spec['root'].prefix),
'SAMINC={0}'.format(spec['samtools'].prefix.include),
'SAMDIR={0}'.format(spec['samtools'].prefix.lib),
'HTSDIR={0}'.format(spec['htslib'].prefix.lib))
def install(self, spec, prefix):
mkdir(prefix.bin)
install('cnvnator', prefix.bin)
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