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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 *
from spack.pkg.builtin.boost import Boost
class Shapeit4(MakefilePackage):
"""SHAPEIT4 is a fast and accurate method for estimation of haplotypes
(aka phasing) for SNP array and high coverage sequencing data."""
homepage = "https://odelaneau.github.io/shapeit4/"
url = "https://github.com/odelaneau/shapeit4/archive/v4.1.3.tar.gz"
version('4.1.3', sha256='d209731277b00bca1e3478b7e0a0cbe40fbe23826c3d640ad12e0dd6033cbbb8')
maintainers = ['ilbiondo']
depends_on('htslib')
# TODO: replace this with an explicit list of components of Boost,
# for instance depends_on('boost +filesystem')
# See https://github.com/spack/spack/pull/22303 for reference
depends_on(Boost.with_default_variants)
depends_on('bzip2')
depends_on('xz')
def edit(self, spec, prefix):
makefile = FileFilter('makefile')
makefile.filter('CXX=.*', 'CXX = c++')
makefile.filter('CXXFLAG=.*', 'CXXFLAG = -O3')
makefile.filter('LDFLAG=.*', 'LDFLAG = -O3')
makefile.filter('HTSLIB_INC=.*', 'HTSLIB_INC = '
+ self.spec['htslib'].prefix.include)
makefile.filter('HTSLIB_LIB=.*', 'HTSLIB_LIB = '
+ self.spec['htslib'].prefix.lib + '/libhts.so')
makefile.filter('BOOST_INC=.*', 'BOOST_INC = '
+ self.spec['boost'].prefix.include)
makefile.filter('BOOST_LIB_IO=.*', 'BOOST_LIB_IO = '
+ self.spec['boost'].prefix.lib
+ "/libboost_iostreams.so")
makefile.filter('BOOST_LIB_PO=.*', 'BOOST_LIB_PO = '
+ self.spec['boost'].prefix.lib
+ "/libboost_program_options.so")
def install(self, spec, prefix):
install_tree('bin', prefix.bin)
install_tree('test', join_path(self.prefix, 'test'))
install_tree('docs', join_path(self.prefix, 'docs'))
install_tree('maps', join_path(self.prefix, 'maps'))
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