eea786f4e8
- remove the old LGPL license headers from all files in Spack - add SPDX headers to all files - core and most packages are (Apache-2.0 OR MIT) - a very small number of remaining packages are LGPL-2.1-only
65 lines
2.8 KiB
Python
65 lines
2.8 KiB
Python
# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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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-3.3.1.tar.gz"
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list_url = "http://bioinf.uni-greifswald.de/augustus/binaries/old"
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version('3.3.1', '8363ece221c799eb169f47e545efb951')
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version('3.3', '93691d9aafc7d3d0e1adf31ec308507f')
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version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830')
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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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if 'bamtools@2.5:' in spec:
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makefile.filter('LIBS = -lbamtools -lz',
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'LIBS = $(BAMTOOLS)/lib64/'
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'/libbamtools.a -lz')
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if 'bamtools@:2.4' in spec:
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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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if 'bamtools@2.5:' in spec:
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makefile.filter('LIBS = -lbamtools -lz',
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'LIBS = $(BAMTOOLS)/lib64/'
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'/libbamtools.a -lz')
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if 'bamtools@:2.4' in spec:
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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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