73 lines
3.3 KiB
Python
73 lines
3.3 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/llnl/spack
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# Please also see the LICENSE file 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 Augustus(MakefilePackage):
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"""AUGUSTUS is a program that predicts genes in eukaryotic
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genomic sequences"""
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homepage = "http://bioinf.uni-greifswald.de/augustus/"
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url = "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.tar.gz"
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version('3.3', '9ebe494df78ebf6a43091cfc8551050c')
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version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830',
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url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.2.3.tar.gz')
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depends_on('bamtools')
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depends_on('gsl')
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depends_on('boost')
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depends_on('zlib')
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def edit(self, spec, prefix):
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with working_dir(join_path('auxprogs', 'filterBam', 'src')):
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makefile = FileFilter('Makefile')
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makefile.filter('BAMTOOLS = .*', 'BAMTOOLS = %s' % self.spec[
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'bamtools'].prefix)
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makefile.filter('INCLUDES = *',
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'INCLUDES = -I$(BAMTOOLS)/include/bamtools ')
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makefile.filter('LIBS = -lbamtools -lz',
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'LIBS = $(BAMTOOLS)/lib/bamtools'
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'/libbamtools.a -lz')
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with working_dir(join_path('auxprogs', 'bam2hints')):
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makefile = FileFilter('Makefile')
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makefile.filter('# Variable definition',
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'BAMTOOLS = %s' % self.spec['bamtools'].prefix)
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makefile.filter('INCLUDES = /usr/include/bamtools',
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'INCLUDES = $(BAMTOOLS)/include/bamtools')
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makefile.filter('LIBS = -lbamtools -lz',
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'LIBS = $(BAMTOOLS)/lib/bamtools'
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'/libbamtools.a -lz')
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def install(self, spec, prefix):
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install_tree('bin', join_path(self.spec.prefix, 'bin'))
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install_tree('config', join_path(self.spec.prefix, 'config'))
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install_tree('scripts', join_path(self.spec.prefix, 'scripts'))
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def setup_environment(self, spack_env, run_env):
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run_env.set('AUGUSTUS_CONFIG_PATH', join_path(
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self.prefix, 'config'))
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run_env.prepend_path('PATH', join_path(self.prefix, 'scripts'))
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