58 lines
1.9 KiB
Python
58 lines
1.9 KiB
Python
# Copyright Spack Project Developers. See 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
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from spack.package 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(
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"2019-11-25",
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sha256="969c0881050c4a48d19be9ea64bf49fa68c1403b69f9f739bbfd865dda639b2d",
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expand=False,
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url="https://faculty.washington.edu/browning/beagle/bref3.25Nov19.28d.jar",
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)
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version(
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"2019-07-12",
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sha256="8a9c3b6c38e36ef4c05a61108f083005fd985026c67d75a8173088f88816a202",
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expand=False,
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url="https://faculty.washington.edu/browning/beagle/bref3.12Jul19.0df.jar",
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)
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version(
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"2018-01-27",
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sha256="4d32f0b6d536c88d5332d961309466c8c3dd9572907a3755450d26d7ba841083",
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expand=False,
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url="https://faculty.washington.edu/browning/beagle/bref.27Jan18.7e1.jar",
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)
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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), script, **kwargs)
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