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# Copyright 2013-2024 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.package import *
class Bref3(Package):
"""Bref3: Converts from VCF format to bref3 format."""
homepage = "https://faculty.washington.edu/browning/beagle/beagle.html"
version(
"2019-11-25",
sha256="969c0881050c4a48d19be9ea64bf49fa68c1403b69f9f739bbfd865dda639b2d",
expand=False,
url="https://faculty.washington.edu/browning/beagle/bref3.25Nov19.28d.jar",
)
version(
"2019-07-12",
sha256="8a9c3b6c38e36ef4c05a61108f083005fd985026c67d75a8173088f88816a202",
expand=False,
url="https://faculty.washington.edu/browning/beagle/bref3.12Jul19.0df.jar",
)
version(
"2018-01-27",
sha256="4d32f0b6d536c88d5332d961309466c8c3dd9572907a3755450d26d7ba841083",
expand=False,
url="https://faculty.washington.edu/browning/beagle/bref.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.
if self.version >= Version("2019"):
script = prefix.bin.bref3
else:
script = prefix.bin.bref
script_sh = join_path(os.path.dirname(__file__), "bref.sh")
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("bref.jar", join_path(prefix.bin, jar_file), script, **kwargs)
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