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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 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 *
import os
import glob
class GenemarkEt(Package):
"""Gene Prediction in Bacteria, archaea, Metagenomes and
Metatranscriptomes."""
homepage = "http://topaz.gatech.edu/GeneMark"
version('4.33', '4ab7d7d3277a685dfb49e11bc5b493c3')
depends_on('perl', type=('build', 'run'))
def url_for_version(self, version):
return "file://{0}/gm_et_linux_64.tar.gz".format(os.getcwd())
def install(self, spec, prefix):
mkdirp(prefix.bin)
with working_dir('gmes_petap'):
install_tree('lib', prefix.lib)
files = glob.iglob('*')
for file in files:
if os.path.isfile(file):
install(file, prefix.bin)
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('PERL5LIB', prefix.lib)
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