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# Copyright 2013-2021 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)
import glob
import os.path
import re
from spack import *
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 = "https://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('2.25.7', sha256='dc0e830d3e838dee2b4f4aa1c9631fb3a4c3ec982de8dfe5145fc748104c7146', expand=False)
version('2.25.6', sha256='768709826514625381e6fa3920945360167f4e830bf72f79eb070da059676f02', expand=False)
version('2.25.5', sha256='f7fa9784b84d384abfcbd77076f5ceab7b2797dc863ac35fd41470daa3efe3a5', expand=False)
version('2.25.4', sha256='c3ac14471e48e28e24201ae5515f828ffa45db7ac3e37173251a672845b4a9b3', expand=False)
version('2.25.3', sha256='1d4dbfcb36d23fde11f173ab0de8a99835e04161efb04f246bbcbfc0bee3b493', expand=False)
version('2.25.2', sha256='aead4baf12028a5d2b9ef70e00c93e4bba8f6bece0b9a7104b89b842a8e0326f', expand=False)
version('2.25.1', sha256='6d6e622d6b465f9fc704c37bcba55b0dac5ad14d07088bbdbdfade5cd027ee1c', expand=False)
version('2.25.0', sha256='faf2434da84fe21b516d57817767920fdedfc19ebdc01d9cae8d6d3314f7e897', expand=False)
version('2.24.0', sha256='70e91039bccc6f6db60f18c41713218a8cdf45f591f02c1012c062152b27cd7b', expand=False)
version('2.20.8', sha256='aff92d618ee9e6bafc1ab4fbfa89fc557a0dbe596ae4b92fe3bf93ebf95c7105', expand=False)
version('2.19.0', sha256='f97fc3f7a73b55cceea8b6a6488efcf1b2fbf8cad61d88645704ddd45a8c5950', expand=False)
version('2.18.3', sha256='0e0fc45d9a822ee9fa562b3bb8f1525a439e4cd541429a1a4ca4646f37189b70', expand=False)
version('2.18.0', sha256='c4c64b39ab47968e4afcaf1a30223445ee5082eab31a03eee240e54c2e9e1dce', expand=False)
version('2.17.0', sha256='ffea8bf90e850919c0833e9dcc16847d40090a1ef733c583a710a3282b925998', expand=False)
version('2.16.0', sha256='01cf3c930d2b4841960497491512d327bf669c1ed2e753152e1e651a27288c2d', expand=False)
version('2.15.0', sha256='dc3ff74c704954a10796b390738078617bb0b0fef15731e9d268ed3b26c6a285', expand=False)
version('2.13.2', sha256='db7749f649e8423053fb971e6af5fb8a9a1a797cb1f20fef1100edf9f82f6f94', expand=False)
version('2.10.0', sha256='e256d5e43656b7d8be454201a7056dce543fe9cbeb30329a0d8c22d28e655775', expand=False)
version('2.9.4', sha256='0ecee9272bd289d902cc18053010f0364d1696e7518ac92419a99b2f0a1cf689', expand=False)
version('2.9.3', sha256='6cca26ce5094b25a82e1a8d646920d584c6db5f009476196dc285be6522e00ce', expand=False)
version('2.9.2', sha256='05714b9743a7685a43c94a93f5d03aa4070d3ab6e20151801301916d3e546eb7', expand=False)
version('2.9.0', sha256='9a57f6bd9086ea0f5f1a6d9d819459854cb883bb8093795c916538ed9dd5de64', expand=False)
version('2.8.3', sha256='97a4b6c8927c8cb5f3450630c9b39bf210ced8c271f198119118ce1c24b8b0f6', expand=False)
version('2.6.0', sha256='671d9e86e6bf0c28ee007aea55d07e2456ae3a57016491b50aab0fd2fd0e493b', expand=False)
version('1.140', sha256='0d27287217413db6b846284c617d502eaa578662dcb054a7017083eab9c54438')
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.txt 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_run_environment(self, env):
"""The Picard docs suggest setting this as a convenience."""
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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