43 lines
1.5 KiB
Python
43 lines
1.5 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 Snphylo(Package):
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"""A pipeline to generate a phylogenetic tree from huge SNP data"""
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homepage = "http://chibba.pgml.uga.edu/snphylo/"
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url = "https://github.com/thlee/SNPhylo/archive/refs/tags/20180901.tar.gz"
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version("20180901", sha256="46273bcafc8f6cc2465fc524926af7dd122bcc7b7ce1b7c3f5c278111c3a9ddd")
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version(
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"2016-02-04",
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sha256="d9e144021c83dbef97bebf743b92109ad0afcfe70f37c244059b43f11b8a50da",
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deprecated=True,
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)
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depends_on("python", type=("build", "run"))
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depends_on("r", type=("build", "run"))
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depends_on("r-phangorn", type=("build", "run"))
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depends_on("r-gdsfmt", type=("build", "run"))
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depends_on("r-snprelate", type=("build", "run"))
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depends_on("r-getopt", type=("build", "run"))
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depends_on("muscle")
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depends_on("phylip")
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def install(self, spec, prefix):
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install_answer = ["y", "y", "y", "y"]
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install_answer_input = "spack-config.in"
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with open(install_answer_input, "w") as f:
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f.writelines(install_answer)
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with open(install_answer_input, "r") as f:
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bash = which("bash")
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bash("./setup.sh", input=f)
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install_tree(".", prefix)
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def setup_run_environment(self, env):
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env.prepend_path("PATH", self.spec.prefix)
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