76 lines
2.9 KiB
Python
76 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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class Mummer(Package):
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"""MUMmer is a system for rapidly aligning entire genomes."""
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homepage = "http://mummer.sourceforge.net/"
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url = "https://sourceforge.net/projects/mummer/files/mummer/3.23/MUMmer3.23.tar.gz/download"
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version('3.23', 'f2422b3d2638dba4baedb71b1acdffa2')
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depends_on('gnuplot')
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depends_on('perl', type=('build', 'run'))
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patch('Makefile.patch')
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patch('scripts-Makefile.patch')
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def patch(self):
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"""Fix mummerplot's use of defined on hashes (deprecated
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since perl@5.10, made illegal in perl@5.20."""
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kwargs = {'string': True}
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filter_file('defined (%', '(%', 'scripts/mummerplot.pl',
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**kwargs)
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def install(self, spec, prefix):
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if self.run_tests:
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make('check')
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make('INSTALL_TOP_DIR={0}'.format(prefix))
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bd = prefix.bin
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abd = join_path(prefix, 'aux_bin')
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sd = join_path(prefix, 'scripts')
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mkdirp(bd)
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mkdirp(abd)
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mkdirp(sd)
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bins = ["show-tiling", "show-snps", "show-coords", "show-aligns",
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"show-diff", "delta-filter", "combineMUMs", "mummer",
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"repeat-match", "annotate", "mgaps", "gaps", "dnadiff",
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"nucmer2xfig", "run-mummer3", "mummerplot", "promer",
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"run-mummer1", "nucmer", "mapview", "exact-tandems"]
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aux_bins = ["aux_bin/postnuc", "aux_bin/postpro",
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"aux_bin/prenuc", "aux_bin/prepro"]
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scripts = ["scripts/Foundation.pm"]
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for f in bins:
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install(f, join_path(bd, f))
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for f in aux_bins:
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install(f, join_path(abd, f[8:]))
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for f in scripts:
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install(f, join_path(sd, f[8:]))
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