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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 Plink2(MakefilePackage):
"""PLINK2: Whole genome association analysis toolset, designed to perform a
range of basic, large-scale analyses in a computationally efficient manner."""
homepage = "https://www.cog-genomics.org/plink/2.0/"
git = "https://github.com/chrchang/plink-ng.git"
version("2.00a4.3", tag="v2.00a4.3", commit="59fca48f6f8135886ff68962fbe31ae0c6413228")
depends_on("zlib-api")
depends_on("zlib@1.2.12:", when="^zlib")
depends_on("zstd@1.5.2:")
depends_on("libdeflate@1.10:")
depends_on("blas")
depends_on("lapack")
build_directory = "2.0/build_dynamic"
def edit(self, spec, prefix):
with working_dir(self.build_directory):
makefile = FileFilter("Makefile")
if "avx2" in spec.target:
makefile.filter(r"^NO_AVX2 = 1", "NO_AVX2 =")
elif "sse4_2" in spec.target:
makefile.filter(r"^NO_SSE42 = 1", "NO_SSE42 =")
makefile.filter(r"^STATIC_ZSTD = 1", "STATIC_ZSTD =")
makefile.filter(
r"^ BLASFLAGS=-llapack -lblas -lcblas -latlas",
" BLASFLAGS={0} {1}".format(
spec["blas"].libs.ld_flags, spec["lapack"].libs.ld_flags
),
)
def build(self, spec, prefix):
with working_dir(self.build_directory):
make()
def install(self, spec, prefix):
mkdir(prefix.bin)
with working_dir(self.build_directory):
install("plink2", prefix.bin)
install("pgen_compress", prefix.bin)
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