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##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class Mummer(Package):
"""MUMmer is a system for rapidly aligning entire genomes."""
homepage = "http://mummer.sourceforge.net/"
url = "https://sourceforge.net/projects/mummer/files/mummer/3.23/MUMmer3.23.tar.gz/download"
version('3.23', 'f2422b3d2638dba4baedb71b1acdffa2')
depends_on('gnuplot')
depends_on('perl', type=('build', 'run'))
patch('Makefile.patch')
patch('scripts-Makefile.patch')
def patch(self):
"""Fix mummerplot's use of defined on hashes (deprecated
since perl@5.10, made illegal in perl@5.20."""
kwargs = {'string': True}
filter_file('defined (%', '(%', 'scripts/mummerplot.pl',
**kwargs)
def install(self, spec, prefix):
if self.run_tests:
make('check')
make('INSTALL_TOP_DIR={0}'.format(prefix))
bd = prefix.bin
abd = join_path(prefix, 'aux_bin')
sd = join_path(prefix, 'scripts')
mkdirp(bd)
mkdirp(abd)
mkdirp(sd)
bins = ["show-tiling", "show-snps", "show-coords", "show-aligns",
"show-diff", "delta-filter", "combineMUMs", "mummer",
"repeat-match", "annotate", "mgaps", "gaps", "dnadiff",
"nucmer2xfig", "run-mummer3", "mummerplot", "promer",
"run-mummer1", "nucmer", "mapview", "exact-tandems"]
aux_bins = ["aux_bin/postnuc", "aux_bin/postpro",
"aux_bin/prenuc", "aux_bin/prepro"]
scripts = ["scripts/Foundation.pm"]
for f in bins:
install(f, join_path(bd, f))
for f in aux_bins:
install(f, join_path(abd, f[8:]))
for f in scripts:
install(f, join_path(sd, f[8:]))
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