68 lines
2.9 KiB
Python
68 lines
2.9 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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import glob
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class Mirdeep(Package):
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"""miRDeep2 is a completely overhauled tool which discovers microRNA genes
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by analyzing sequenced RNAs."""
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homepage = "https://www.mdc-berlin.de/8551903/en/"
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url = "https://www.mdc-berlin.de/45995549/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/mirdeep2_0_0_8.zip"
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version('2.0.0.8', 'a707f7d7ad4a2975fb8b2e78c5bcf483')
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depends_on('perl', type=('build', 'run'))
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depends_on('perl-pdf-api2', type=('build', 'run'))
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depends_on('bowtie')
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depends_on('viennarna')
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depends_on('squid')
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depends_on('randfold')
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def url_for_version(self, version):
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url = 'https://www.mdc-berlin.de/45995549/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/mirdeep{0}.zip'
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return url.format(version.underscored)
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def patch(self):
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with working_dir('src'):
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files = glob.iglob("*.pl")
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for file in files:
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change = FileFilter(file)
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change.filter('usr/bin/perl', 'usr/bin/env perl')
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change.filter('perl -W', 'perl')
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change.filter("../Rfam_for_miRDeep.fa",
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"Rfam_for_miRDeep.fa")
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change.filter("../install_successful",
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"install_successful")
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def install(self, spec, prefix):
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install_tree('src', prefix.bin)
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install('Rfam_for_miRDeep.fa', prefix.bin)
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# miRDeep looks for the install_sucessful file to check if you used
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# their automated install script which we'll just be kind of hacking
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# around
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touch(prefix.bin.install_successful)
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