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