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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 Braker(Package):
"""BRAKER is a pipeline for unsupervised RNA-Seq-based genome annotation
that combines the advantages of GeneMark-ET and AUGUSTUS"""
homepage = "http://exon.gatech.edu/braker1.html"
url = "http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1_v1.11.tar.gz"
version('1.11', '297efe4cabdd239b710ac2c45d81f6a5')
depends_on('perl', type=('build', 'run'))
depends_on('augustus')
depends_on('genemark-et')
depends_on('bamtools')
depends_on('samtools')
def install(self, spec, prefix):
mkdirp(prefix.bin)
mkdirp(prefix.lib)
install('braker.pl', prefix.bin)
install('filterGenemark.pl', prefix.bin)
install('filterIntronsFindStrand.pl', prefix.bin)
install('helpMod.pm', prefix.lib)
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('PERL5LIB', prefix.lib)
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