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##############################################################################
# Copyright (c) 2013-2018, 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 shutil import copyfile
import os
class Igvtools(Package):
"""IGVTools suite of command-line utilities for preprocessing data
files"""
homepage = "https://software.broadinstitute.org/software/igv/home"
url = "http://data.broadinstitute.org/igv/projects/downloads/2.3/igvtools_2.3.98.zip"
version('2.3.98', '17ed12a213cd9cdaeb2f2a5c56d84bc4')
depends_on('java@8:')
def install(self, spec, prefix):
mkdirp(prefix.bin)
jar_file = 'igvtools.jar'
install(jar_file, prefix.bin)
install_tree('genomes', prefix.genomes)
# 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__), "igvtools.sh")
script = join_path(prefix.bin, "igvtools")
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['jdk'].prefix, 'bin', 'java')
kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
filter_file('^java', java, script, **kwargs)
filter_file(jar_file, join_path(prefix.bin, jar_file),
script, **kwargs)
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