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| -rw-r--r-- | var/spack/repos/builtin/packages/augustus/package.py | 70 |
1 files changed, 70 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py new file mode 100644 index 0000000000..ccaa2f1e70 --- /dev/null +++ b/var/spack/repos/builtin/packages/augustus/package.py @@ -0,0 +1,70 @@ +############################################################################## +# 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')) |