40 lines
1.3 KiB
Python
40 lines
1.3 KiB
Python
# Copyright 2013-2023 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 Haploview(Package):
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"""Haploview is designed to simplify and expedite the process of haplotype
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analysis."""
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homepage = "https://www.broadinstitute.org/haploview/haploview"
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url = "https://downloads.sourceforge.net/project/haploview/release/Haploview4.1.jar"
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version(
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"4.1",
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sha256="b3ffe4c3d8bbab6af5eebf89a2dccdb185280088f70ae84c84be60f85f10201d",
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expand=False,
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)
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depends_on("java", type=("build", "run"))
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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jar_file = "Haploview{v}.jar".format(v=self.version)
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install(jar_file, prefix.bin)
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script_sh = join_path(os.path.dirname(__file__), "haploview.sh")
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script = prefix.bin.haploview
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install(script_sh, script)
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set_executable(script)
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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("haploview.jar", join_path(prefix.bin, jar_file), script, **kwargs)
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