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# Copyright 2013-2023 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 Pilon(Package):
"""Pilon is an automated genome assembly improvement and variant
detection tool."""
homepage = "https://github.com/broadinstitute/pilon"
url = "https://github.com/broadinstitute/pilon/releases/download/v1.22/pilon-1.22.jar"
version(
"1.22",
sha256="ff738f3bbb964237f6b2cf69243ebf9a21cb7f4edf10bbdcc66fa4ebaad5d13d",
expand=False,
)
version(
"1.13",
sha256="c6195a054acbc76afc457e6a7615f75c91adc28faeb7b8738ee2b65309b0bbe3",
expand=False,
)
depends_on("java@1.7:", type="run")
def install(self, spec, prefix):
mkdirp(prefix.bin)
jar_file = "pilon-{0}.jar".format(self.version.dotted)
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__), "pilon.sh")
script = prefix.bin.pilon
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("pilon-{0}.jar", join_path(prefix.bin, jar_file), script, **kwargs)
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