23aed605ec
* Adding additional versions to plink2 and switching to tarballs to allow for better version detection in the future --------- Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
59 lines
2.2 KiB
Python
59 lines
2.2 KiB
Python
# Copyright 2013-2024 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.package import *
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class Plink2(MakefilePackage):
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"""PLINK2: Whole genome association analysis toolset, designed to perform a
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range of basic, large-scale analyses in a computationally efficient manner."""
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homepage = "https://www.cog-genomics.org/plink/2.0/"
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url = "https://github.com/chrchang/plink-ng/archive/refs/tags/v2.00a5.11.tar.gz"
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list_url = "https://github.com/chrchang/plink-ng/tags"
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maintainers("teaguesterling")
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license("GPLv3", checked_by="teaguesterling")
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# See: https://github.com/chrchang/plink-ng/blob/master/2.0/COPYING
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version("2.00a5.11", sha256="8b664baa0b603f374123c32818ea2f053272840ba60e998d06cb864f3a6f1c38")
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version("2.00a5.10", sha256="53d845c6a04f8fc701e6f58f6431654e36cbf6b79bff25099862d169a8199a45")
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version("2.00a4.3", sha256="3cd1d26ac6dd1c451b42440f479789aa19d2b57642c118aac530a5ff1b0b4ce6")
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depends_on("zlib-api")
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depends_on("zlib@1.2.12:", when="^[virtuals=zlib-api] zlib")
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depends_on("zstd@1.5.2:")
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depends_on("libdeflate@1.10:")
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depends_on("blas")
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depends_on("lapack")
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build_directory = "2.0/build_dynamic"
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def edit(self, spec, prefix):
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with working_dir(self.build_directory):
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makefile = FileFilter("Makefile")
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if "avx2" in spec.target:
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makefile.filter(r"^NO_AVX2 = 1", "NO_AVX2 =")
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elif "sse4_2" in spec.target:
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makefile.filter(r"^NO_SSE42 = 1", "NO_SSE42 =")
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makefile.filter(r"^STATIC_ZSTD = 1", "STATIC_ZSTD =")
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makefile.filter(
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r"^ BLASFLAGS=-llapack -lblas -lcblas -latlas",
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" BLASFLAGS={0} {1}".format(
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spec["blas"].libs.ld_flags, spec["lapack"].libs.ld_flags
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),
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)
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def build(self, spec, prefix):
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with working_dir(self.build_directory):
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make()
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def install(self, spec, prefix):
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mkdir(prefix.bin)
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with working_dir(self.build_directory):
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install("plink2", prefix.bin)
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install("pgen_compress", prefix.bin)
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