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# Copyright 2013-2021 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 PlinkNg(Package):
"""A comprehensive update to the PLINK association analysis toolset."""
homepage = "https://www.cog-genomics.org/plink/2.0/"
url = "https://www.cog-genomics.org/static/bin/plink2_src_200511.zip"
version('200511', sha256='00cff19bece88acb7a21ba098501cb677b78d22c9f3ca5bcdc869139a40db816')
depends_on('zlib')
depends_on('zstd@1.4.4:')
depends_on('cblas')
depends_on('blas')
depends_on('lapack')
conflicts('%gcc@:4')
def url_for_version(self, ver):
template = 'https://www.cog-genomics.org/static/bin/plink2_src_{0}.zip'
return template.format(ver)
def setup_build_environment(self, env):
zlib = join_path(self.spec['zlib'].prefix.lib, 'libz.a')
env.set('ZLIB', zlib)
def install(self, spec, prefix):
ld_flags = [spec['lapack'].libs.ld_flags, spec['blas'].libs.ld_flags]
filter_file('-llapack -lcblas -lblas', ' '.join(ld_flags),
'build.sh', string=True)
which('sh')('build.sh')
install_tree('.', prefix)
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