57 lines
1.6 KiB
Python
57 lines
1.6 KiB
Python
# Copyright 2013-2019 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 Bracken(Package):
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"""Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly
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accurate statistical method that computes the abundance of species in DNA
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sequences from a metagenomics sample."""
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homepage = "https://ccb.jhu.edu/software/bracken"
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url = "https://github.com/jenniferlu717/Bracken/archive/1.0.0.tar.gz"
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version('1.0.0', 'bd91805655269c5f3becb8f8028bab6d')
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depends_on('perl')
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depends_on('python@2.7:')
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depends_on('perl-exporter-tiny')
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depends_on('perl-list-moreutils')
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depends_on('perl-parallel-forkmanager')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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install_tree('sample_data', prefix.sample_data)
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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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'count-kmer-abundances.pl'
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)
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filter_file(
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r'#!/usr/bin/python',
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'#!/usr/bin/env python',
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'est_abundance.py'
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)
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filter_file(
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r'#!/usr/bin/python',
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'#!/usr/bin/env python',
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'generate_kmer_distribution.py'
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)
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files = (
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'count-kmer-abundances.pl',
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'est_abundance.py',
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'generate_kmer_distribution.py',
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)
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chmod = which('chmod')
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for name in files:
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install(name, prefix.bin)
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chmod('+x', join_path(self.prefix.bin, name))
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