bafd84e191
* Switch http to https where latter exists * Hopefully restore original permissions * Add URL updates after include the -L curl option * Manual corrections to select URL format strings
45 lines
1.9 KiB
Python
45 lines
1.9 KiB
Python
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import os.path
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from spack import *
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class Beagle(Package):
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"""Beagle is a software package for phasing genotypes and for imputing
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ungenotyped markers."""
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homepage = "https://faculty.washington.edu/browning/beagle/beagle.html"
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version('5.1', sha256='994f926a4ec0eac665631f37c4a961d3f75c966c71841079275364013c90996c',
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expand=False, url='https://faculty.washington.edu/browning/beagle/beagle.25Nov19.28d.jar')
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version('5.0', sha256='8390fe18b53786b676b67dddae6d1c086d6225e518f6a82047f4138196b48621',
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expand=False, url='https://faculty.washington.edu/browning/beagle/beagle.12Jul19.0df.jar')
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version('4.1', sha256='6c94610b278fc108c3e80b1134226911be1fc92b7d378ba648ac3eb97c5a3207',
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expand=False, url='https://faculty.washington.edu/browning/beagle/beagle.27Jan18.7e1.jar')
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depends_on('java@8', type='run')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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jar_file = os.path.basename(self.stage.archive_file)
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install(jar_file, prefix.bin)
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# Set up a helper script to call java on the jar file,
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# explicitly codes the path for java and the jar file.
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script_sh = join_path(os.path.dirname(__file__), "beagle.sh")
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script = prefix.bin.beagle
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install(script_sh, script)
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set_executable(script)
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# Munge the helper script to explicitly point to java and the
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# jar file.
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java = self.spec['java'].prefix.bin.java
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kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
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filter_file('^java', java, script, **kwargs)
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filter_file('beagle.jar', join_path(prefix.bin, jar_file),
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script, **kwargs)
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