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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 *
from distutils.dir_util import copy_tree
from shutil import copyfile
import os.path
class Trimmomatic(Package):
"""A flexible read trimming tool for Illumina NGS data."""
homepage = "http://www.usadellab.org/cms/?page=trimmomatic"
url = "http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip"
# Older version aren't explicitly made available, but the URL
# works as we'd like it to, so...
version('0.36', '8549130d86b6f0382b1a71a2eb45de39')
version('0.33', '924fc8eb38fdff71740a0e05d32d6a2b')
depends_on('java@8:', type='run')
def install(self, spec, prefix):
mkdirp(prefix.bin)
jar_file = 'trimmomatic-{v}.jar'.format(v=self.version.dotted)
install(jar_file, prefix.bin)
# Put the adapter files someplace sensible
copy_tree('adapters', join_path(self.prefix.share, 'adapters'))
# Set up a helper script to call java on the jar file,
# explicitly codes the path for java and the jar file.
script_sh = join_path(os.path.dirname(__file__), "trimmomatic.sh")
script = join_path(prefix.bin, "trimmomatic")
copyfile(script_sh, script)
set_executable(script)
# Munge the helper script to explicitly point to java and the
# jar file.
java = join_path(self.spec['java'].prefix, 'bin', 'java')
kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
filter_file('^java', java, script, **kwargs)
filter_file('trimmomatic.jar', join_path(prefix.bin, jar_file),
script, **kwargs)
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