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
48 lines
1.9 KiB
Python
48 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 Bref3(Package):
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"""Bref3: Converts from VCF format to bref3 format."""
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homepage = "https://faculty.washington.edu/browning/beagle/beagle.html"
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version('2019-11-25', sha256='969c0881050c4a48d19be9ea64bf49fa68c1403b69f9f739bbfd865dda639b2d',
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expand=False, url='https://faculty.washington.edu/browning/beagle/bref3.25Nov19.28d.jar')
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version('2019-07-12', sha256='8a9c3b6c38e36ef4c05a61108f083005fd985026c67d75a8173088f88816a202',
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expand=False, url='https://faculty.washington.edu/browning/beagle/bref3.12Jul19.0df.jar')
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version('2018-01-27', sha256='4d32f0b6d536c88d5332d961309466c8c3dd9572907a3755450d26d7ba841083',
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expand=False, url='https://faculty.washington.edu/browning/beagle/bref.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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if self.version >= Version('2019'):
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script = prefix.bin.bref3
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else:
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script = prefix.bin.bref
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script_sh = join_path(os.path.dirname(__file__), "bref.sh")
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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('bref.jar', join_path(prefix.bin, jar_file),
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script, **kwargs)
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