44 lines
1.4 KiB
Python
44 lines
1.4 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 FrHit(Package):
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"""An efficient algorithm for fragment recruitment for next generation
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sequences against microbial reference genomes."""
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homepage = "http://weizhong-lab.ucsd.edu/frhit"
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url = "http://weizhong-lab.ucsd.edu/frhit/fr-hit-v0.7.1-2013-02-20.tar.gz"
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license("MIT")
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version(
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"0.7.1-2013-02-20",
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sha256="44dcfeb73106529fcefb02c017ec7b95b04b6523a2a57683b2bc905c142e62eb",
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)
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depends_on("perl")
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depends_on("python@2.7:")
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# The patch adds the python interpreter to the beginning of the script
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# allowing it to be run directly without passing the entire path to the
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# script to python.
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patch("binning.patch")
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def install(self, spec, prefix):
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make()
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filter_file(r"#!/bin/env perl", "#!/usr/bin/env perl", "frhit2pairend.pl")
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filter_file(r"#!/bin/env perl", "#!/usr/bin/env perl", "psl2sam.pl")
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mkdirp(prefix.bin)
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install("fr-hit", prefix.bin)
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install("frhit2pairend.pl", prefix.bin)
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install("psl2sam.pl", prefix.bin)
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install("binning-1.1.1/bacteria_gitax.pkl", prefix.bin)
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install("binning-1.1.1/binning.py", prefix.bin)
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install("binning-1.1.1/tax.pkl", prefix.bin)
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