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# Copyright 2013-2024 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.package 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-api")
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-api"].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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