47 lines
1.5 KiB
Python
47 lines
1.5 KiB
Python
# Copyright 2013-2020 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 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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version('0.7.1-2013-02-20', sha256='44dcfeb73106529fcefb02c017ec7b95b04b6523a2a57683b2bc905c142e62eb')
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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(
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r'#!/bin/env perl',
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'#!/usr/bin/env perl',
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'frhit2pairend.pl'
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)
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filter_file(
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r'#!/bin/env perl',
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'#!/usr/bin/env perl',
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'psl2sam.pl'
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)
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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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