45 lines
1.5 KiB
Python
45 lines
1.5 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.path
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from spack.package import *
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class Snpeff(Package, SourceforgePackage):
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"""SnpEff is a variant annotation and effect prediction tool. It
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annotates and predicts the effects of genetic variants (such as
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amino acid changes)."""
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homepage = "https://snpeff.sourceforge.net/"
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sourceforge_mirror_path = "snpeff/snpEff_latest_core.zip"
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version(
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"2017-11-24", sha256="d55a7389a78312947c1e7dadf5e6897b42d3c6e942e7c1b8ec68bb35d2ae2244"
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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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install_tree("snpEff", prefix.bin)
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# Set up a helper script to call java on the jar files,
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# explicitly codes the path for java and the jar files.
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scripts = ["snpEff", "SnpSift"]
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for script in scripts:
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script_sh = join_path(os.path.dirname(__file__), script + ".sh")
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script_path = join_path(prefix.bin, script)
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install(script_sh, script_path)
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set_executable(script_path)
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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 = {"backup": False}
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filter_file("^java", java, script_path, **kwargs)
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filter_file(
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script + ".jar", join_path(prefix.bin, script + ".jar"), script_path, **kwargs
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)
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