69 lines
2.9 KiB
Python
69 lines
2.9 KiB
Python
##############################################################################
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# Copyright (c) 2013-2018, 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 Mitofates(Package):
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"""MitoFates predicts mitochondrial presequence, a cleavable localization
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signal located in N-terminal, and its cleaved position."""
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homepage = "http://mitf.cbrc.jp/MitoFates/cgi-bin/top.cgi"
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url = "http://mitf.cbrc.jp/MitoFates/program/MitoFates_1.2.tar.gz"
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version('1.2', 'aaac42a8e8c7318a4abde9df3a4b72d1')
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depends_on('libsvm')
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depends_on('perl', type='run')
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depends_on('perl-inline-c', type='run')
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depends_on('perl-perl6-slurp', type='run')
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depends_on('perl-math-cephes', type='run')
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# The DirichletRegulator_fast.pm sets the perl Inline directory
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# to be inside the deployed source (which won't be writable by
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# the end user of site wide deployed software.
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# Removing that config entry will cause the inline module to auto
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# create a directory in the user's homedir instead
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patch('DirichletRegulator_fast.patch')
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def patch(self):
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perlscripts = FileFilter('MitoFates.pl')
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perlscripts.filter('#!/usr/bin/perl', '#!/usr/bin/env perl')
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# other perl module files probably should get this filter too
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with working_dir(join_path(self.stage.source_path, 'bin/modules')):
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perlmodules = glob.glob('*.pm')
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filter_file('#!/usr/bin/perl', '#!/usr/bin/env perl', *perlmodules)
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def install(self, spec, prefix):
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install_tree('bin', prefix.bin)
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install('MitoFates.pl', prefix)
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chmod = which('chmod')
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chmod('+x', join_path(prefix, 'MitoFates.pl'))
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def setup_environment(self, spack_env, run_env):
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# We want the main MitoFates.pl script in the path
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run_env.prepend_path('PATH', self.prefix)
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