72 lines
2.5 KiB
Python
72 lines
2.5 KiB
Python
# Copyright 2013-2023 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 Plink(Package):
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"""PLINK is a free, open-source whole genome association analysis toolset,
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designed to perform a range of basic, large-scale analyses in a
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computationally efficient manner."""
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homepage = "https://www.cog-genomics.org/plink/1.9/"
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version(
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"1.9-beta6.27",
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commit="a2ea957c893fbb0558358edef27f3ecbf3d360f8",
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git="https://github.com/chrchang/plink-ng.git",
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)
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version(
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"1.9-beta6.10",
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sha256="f8438656996c55a5edd95c223cce96277de6efaab1b9b1d457bfee0c272058d8",
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url="https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20190617.zip",
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)
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version(
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"1.9-beta5",
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sha256="e00ef16ac5abeb6b4c4d77846bd655fafc62669fbebf8cd2e941f07b3111907e",
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url="https://github.com/chrchang/plink-ng/archive/b15c19f.tar.gz",
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)
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version(
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"1.07",
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sha256="70c52ee47eed854293832639dbabb41c7c036db3a4881c136e6a71ecff4ac7f4",
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url="https://zzz.bwh.harvard.edu/plink/dist/plink-1.07-x86_64.zip",
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preferred=True,
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)
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depends_on("atlas", when="@1.9-beta5:1.9-beta6.10")
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depends_on("netlib-lapack", when="@1.9-beta5:1.9-beta6.10")
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with when("@1.9-beta-6.27:"):
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depends_on("zlib", when="@1.9-beta6.27:")
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depends_on("blas", when="@1.9-beta6.27:")
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depends_on("lapack", when="@1.9-beta6.27:")
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patch("dynamic_zlib.patch", when="@1.9-beta6.27:")
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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if spec.version == Version("1.07"):
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install("plink", prefix.bin)
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install("gPLINK.jar", prefix.bin)
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if spec.version == Version("1.9-beta5"):
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with working_dir("1.9"):
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first_compile = Executable("./plink_first_compile")
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first_compile()
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install("plink", prefix.bin)
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if spec.version == Version("1.9-beta6.10"):
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install("plink", prefix.bin)
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@when("@1.9-beta6.27:")
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def setup_build_environment(self, env):
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env.set("BLASFLAGS", self.spec["blas"].libs.ld_flags)
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env.set("ZLIB", self.spec["zlib"].libs.ld_flags)
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@when("@1.9-beta6.27:")
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def install(self, spec, prefix):
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with working_dir("1.9"):
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make()
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mkdir(prefix.bin)
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install("plink", prefix.bin)
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