49 lines
1.6 KiB
Python
49 lines
1.6 KiB
Python
# Copyright 2013-2024 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.package import *
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class Pilon(Package):
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"""Pilon is an automated genome assembly improvement and variant
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detection tool."""
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homepage = "https://github.com/broadinstitute/pilon"
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url = "https://github.com/broadinstitute/pilon/releases/download/v1.22/pilon-1.22.jar"
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version(
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"1.22",
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sha256="ff738f3bbb964237f6b2cf69243ebf9a21cb7f4edf10bbdcc66fa4ebaad5d13d",
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expand=False,
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)
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version(
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"1.13",
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sha256="c6195a054acbc76afc457e6a7615f75c91adc28faeb7b8738ee2b65309b0bbe3",
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expand=False,
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)
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depends_on("java@1.7:", type="run")
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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jar_file = "pilon-{0}.jar".format(self.version.dotted)
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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__), "pilon.sh")
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script = prefix.bin.pilon
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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("pilon-{0}.jar", join_path(prefix.bin, jar_file), script, **kwargs)
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