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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 shutil import copyfile
import glob
import os.path
import re
class Picard(Package):
"""Picard is a set of command line tools for manipulating high-throughput
sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
"""
homepage = "http://broadinstitute.github.io/picard/"
url = "https://github.com/broadinstitute/picard/releases/download/2.9.2/picard.jar"
# They started distributing a single jar file at v2.6.0, prior to
# that it was a .zip file with multiple .jar and .so files
version('2.9.2', '0449279a6a89830917e8bcef3a976ef7', expand=False,
url="https://github.com/broadinstitute/picard/releases/download/2.9.2/picard.jar")
version('1.140', '308f95516d94c1f3273a4e7e2b315ec2',
url='https://github.com/broadinstitute/picard/releases/download/1.140/picard-tools-1.140.zip')
depends_on('java@8:', type='run')
def install(self, spec, prefix):
mkdirp(prefix.bin)
# The list of files to install varies with release...
# ... but skip the spack-{build.env}.out files.
files = [x for x in glob.glob("*") if not re.match("^spack-", x)]
for f in files:
install(f, prefix.bin)
# 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__), "picard.sh")
script = join_path(prefix.bin, "picard")
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('picard.jar', join_path(prefix.bin, 'picard.jar'),
script, **kwargs)
def setup_environment(self, spack_env, run_env):
"""The Picard docs suggest setting this as a convenience."""
run_env.prepend_path('PICARD',
join_path(self.prefix, 'bin', 'picard.jar'))
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