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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 os.path
from spack import *
class Beagle(Package):
"""Beagle is a software package for phasing genotypes and for imputing
ungenotyped markers."""
homepage = "https://faculty.washington.edu/browning/beagle/beagle.html"
version('5.1', sha256='994f926a4ec0eac665631f37c4a961d3f75c966c71841079275364013c90996c',
expand=False, url='https://faculty.washington.edu/browning/beagle/beagle.25Nov19.28d.jar')
version('5.0', sha256='8390fe18b53786b676b67dddae6d1c086d6225e518f6a82047f4138196b48621',
expand=False, url='https://faculty.washington.edu/browning/beagle/beagle.12Jul19.0df.jar')
version('4.1', sha256='6c94610b278fc108c3e80b1134226911be1fc92b7d378ba648ac3eb97c5a3207',
expand=False, url='https://faculty.washington.edu/browning/beagle/beagle.27Jan18.7e1.jar')
depends_on('java@8', type='run')
def install(self, spec, prefix):
mkdirp(prefix.bin)
jar_file = os.path.basename(self.stage.archive_file)
install(jar_file, 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__), "beagle.sh")
script = prefix.bin.beagle
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('beagle.jar', join_path(prefix.bin, jar_file),
script, **kwargs)
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