e3c708fafe
* prinseq-lite: Create new package * prinseq-lite: set variant description and add dependency type
61 lines
2.4 KiB
Python
61 lines
2.4 KiB
Python
##############################################################################
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# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/spack/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class PrinseqLite(Package):
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"""PRINSEQ will help you to preprocess your genomic or metagenomic
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sequence data in FASTA or FASTQ format."""
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homepage = "http://prinseq.sourceforge.net"
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url = "https://sourceforge.net/projects/prinseq/files/standalone/prinseq-lite-0.20.4.tar.gz"
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version('0.20.4', '3be1a572073ebbbecfeba42a42853ff5')
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variant('nopca', default=True, description="Graphs version without PCA")
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depends_on('perl', type='run')
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depends_on('perl-cairo', type='run')
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depends_on('perl-digest-md5', type='run')
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depends_on('perl-json', type='run')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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filter_file(r'#!/usr/bin/perl',
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'#!/usr/bin/env perl',
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'prinseq-graphs-noPCA.pl')
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filter_file(r'#!/usr/bin/perl',
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'#!/usr/bin/env perl',
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'prinseq-lite.pl')
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install('prinseq-graphs-noPCA.pl', prefix.bin)
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install('prinseq-lite.pl', prefix.bin)
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chmod = which('chmod')
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chmod('+x', join_path(self.prefix.bin, 'prinseq-graphs-noPCA.pl'))
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chmod('+x', join_path(self.prefix.bin, 'prinseq-lite.pl'))
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