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# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
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"
_urlfmt = "https://github.com/broadinstitute/picard/releases/download/{0}/picard.jar"
_oldurlfmt = 'https://github.com/broadinstitute/picard/releases/download/{0}/picard-tools-{0}.zip'
# 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('2.18.3', '181b1b0731fd35f0d8bd44677d8787e9', expand=False)
version('2.18.0', '20045ff141e4a67512365f0b6bbd8229', expand=False)
version('2.17.0', '72cc527f1e4ca6a799ae0117af60b54e', expand=False)
version('2.16.0', 'fed8928b03bb36e355656f349e579083', expand=False)
version('2.15.0', '3f5751630b1a3449edda47a0712a64e4', expand=False)
version('2.13.2', '3d7b33fd1f43ad2129e6ec7883af56f5', expand=False)
version('2.10.0', '96f3c11b1c9be9fc8088bc1b7b9f7538', expand=False)
version('2.9.4', '5ce72af4d5efd02fba7084dcfbb3c7b3', expand=False)
version('2.9.3', '3a33c231bcf3a61870c3d44b3b183924', expand=False)
version('2.9.2', '0449279a6a89830917e8bcef3a976ef7', expand=False)
version('2.9.0', 'b711d492f16dfe0084d33e684dca2202', expand=False)
version('2.8.3', '4a181f55d378cd61d0b127a40dfd5016', expand=False)
version('2.6.0', '91f35f22977d9692ce2718270077dc50', expand=False)
version('1.140', '308f95516d94c1f3273a4e7e2b315ec2')
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 = prefix.bin.picard
install(script_sh, script)
set_executable(script)
# Munge the helper script to explicitly point to java and the
# jar file.
java = 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'))
def url_for_version(self, version):
if version < Version('2.6.0'):
return self._oldurlfmt.format(version)
else:
return self._urlfmt.format(version)
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