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-rw-r--r--var/spack/repos/builtin/packages/augustus/package.py70
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diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py
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+##############################################################################
+# Copyright (c) 2013-2016, 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/llnl/spack
+# Please also see the LICENSE file 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 Augustus(MakefilePackage):
+ """AUGUSTUS is a program that predicts genes in eukaryotic
+ genomic sequences"""
+
+ homepage = "http://bioinf.uni-greifswald.de/augustus/"
+ url = "http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.2.3.tar.gz"
+
+ version('3.2.3', 'b8c47ea8d0c45aa7bb9a82626c8ff830')
+
+ depends_on('bamtools')
+ depends_on('gsl')
+ depends_on('boost')
+ depends_on('zlib')
+
+ def edit(self, spec, prefix):
+ with working_dir(join_path('auxprogs', 'filterBam', 'src')):
+ makefile = FileFilter('Makefile')
+ makefile.filter('BAMTOOLS = .*', 'BAMTOOLS = %s' % self.spec[
+ 'bamtools'].prefix)
+ makefile.filter('INCLUDES = *',
+ 'INCLUDES = -I$(BAMTOOLS)/include/bamtools ')
+ makefile.filter('LIBS = -lbamtools -lz',
+ 'LIBS = $(BAMTOOLS)/lib/bamtools'
+ '/libbamtools.a -lz')
+ with working_dir(join_path('auxprogs', 'bam2hints')):
+ makefile = FileFilter('Makefile')
+ makefile.filter('# Variable definition',
+ 'BAMTOOLS = %s' % self.spec['bamtools'].prefix)
+ makefile.filter('INCLUDES = /usr/include/bamtools',
+ 'INCLUDES = $(BAMTOOLS)/include/bamtools')
+ makefile.filter('LIBS = -lbamtools -lz',
+ 'LIBS = $(BAMTOOLS)/lib/bamtools'
+ '/libbamtools.a -lz')
+
+ def install(self, spec, prefix):
+ install_tree('bin', join_path(self.spec.prefix, 'bin'))
+ install_tree('config', join_path(self.spec.prefix, 'config'))
+ install_tree('scripts', join_path(self.spec.prefix, 'scripts'))
+
+ def setup_environment(self, spack_env, run_env):
+ run_env.set('AUGUSTUS_CONFIG_PATH', join_path(
+ self.prefix, 'config'))
+ run_env.prepend_path('PATH', join_path(self.prefix, 'scripts'))