a8ccb8e116
- [x] add `concretize.lp`, `spack.yaml`, etc. to licensed files
- [x] update all licensed files to say 2013-2021 using
`spack license update-copyright-year`
- [x] appease mypy with some additions to package.py that needed
for oneapi.py
56 lines
1.9 KiB
Python
56 lines
1.9 KiB
Python
# Copyright 2013-2021 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 Shapeit4(MakefilePackage):
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"""SHAPEIT4 is a fast and accurate method for estimation of haplotypes
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(aka phasing) for SNP array and high coverage sequencing data."""
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homepage = "https://odelaneau.github.io/shapeit4/"
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url = "https://github.com/odelaneau/shapeit4/archive/v4.1.3.tar.gz"
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version('4.1.3', sha256='d209731277b00bca1e3478b7e0a0cbe40fbe23826c3d640ad12e0dd6033cbbb8')
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maintainers = ['ilbiondo']
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depends_on('htslib')
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depends_on('boost')
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depends_on('bzip2')
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depends_on('xz')
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def edit(self, spec, prefix):
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makefile = FileFilter('makefile')
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makefile.filter('CXX=.*', 'CXX = c++')
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makefile.filter('CXXFLAG=.*', 'CXXFLAG = -O3')
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makefile.filter('LDFLAG=.*', 'LDFLAG = -O3')
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makefile.filter('HTSLIB_INC=.*', 'HTSLIB_INC = '
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+ self.spec['htslib'].prefix.include)
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makefile.filter('HTSLIB_LIB=.*', 'HTSLIB_LIB = '
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+ self.spec['htslib'].prefix.lib + '/libhts.so')
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makefile.filter('BOOST_INC=.*', 'BOOST_INC = '
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+ self.spec['boost'].prefix.include)
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makefile.filter('BOOST_LIB_IO=.*', 'BOOST_LIB_IO = '
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+ self.spec['boost'].prefix.lib
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+ "/libboost_iostreams.so")
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makefile.filter('BOOST_LIB_PO=.*', 'BOOST_LIB_PO = '
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+ self.spec['boost'].prefix.lib
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+ "/libboost_program_options.so")
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def install(self, spec, prefix):
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install_tree('bin', prefix.bin)
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install_tree('test', join_path(self.prefix, 'test'))
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install_tree('docs', join_path(self.prefix, 'docs'))
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install_tree('maps', join_path(self.prefix, 'maps'))
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