26a62a3258
- constrain samtools to version 1.13 - replace lzma dependency with xz - add missing dependencies for libdeflate and openssl - explicitly set LD_FLAGS for dependencies in makefile
62 lines
2.2 KiB
Python
62 lines
2.2 KiB
Python
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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class Cnvnator(MakefilePackage):
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"""A tool for CNV discovery and genotyping
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from depth-of-coverage by mapped reads."""
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homepage = "https://github.com/abyzovlab/CNVnator"
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url = "https://github.com/abyzovlab/CNVnator/archive/v0.3.3.tar.gz"
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version('0.3.3', sha256='58c5acf61f9a1e5febf546c196f8917a5e084b729e5c4cfd3eba83471b3fe5c1')
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depends_on('samtools@:1.13')
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depends_on('htslib')
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depends_on('root')
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depends_on('bzip2')
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depends_on('curl')
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depends_on('xz')
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depends_on('zlib')
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depends_on('libdeflate')
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depends_on('openssl')
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def edit(self, spec, prefix):
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makefile = FileFilter('Makefile')
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# Replace -fopenmp with self.compiler.openmp_flag
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makefile.filter('-fopenmp', self.compiler.openmp_flag)
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# Replace CXX with CXXFLAGS
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makefile.filter('CXX.*=.*',
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r'CXXFLAGS = -DCNVNATOR_VERSION=\"$(VERSION)\"'
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' $(OMPFLAGS)'
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' {0}'.format(self.compiler.cxx11_flag))
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makefile.filter('$(CXX)', '$(CXX) $(CXXFLAGS)', string=True)
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# Replace -I$(SAMDIR) with -I$(SAMINC)
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makefile.filter('-I$(SAMDIR)', '-I$(SAMINC)', string=True)
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# Link more libs
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ldflags = [
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spec['zlib'].libs.ld_flags,
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spec['bzip2'].libs.ld_flags,
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spec['curl'].libs.ld_flags,
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spec['xz'].libs.ld_flags,
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spec['libdeflate'].libs.ld_flags,
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spec['openssl'].libs.ld_flags,
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]
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makefile.filter('^override LIBS.*',
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'override LIBS += {0}'.format(' '.join(ldflags)))
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def build(self, spec, prefix):
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make('ROOTSYS={0}'.format(spec['root'].prefix),
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'SAMINC={0}'.format(spec['samtools'].prefix.include),
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'SAMDIR={0}'.format(spec['samtools'].prefix.lib),
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'HTSDIR={0}'.format(spec['htslib'].prefix.lib))
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def install(self, spec, prefix):
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mkdir(prefix.bin)
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install('cnvnator', prefix.bin)
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