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# Copyright 2013-2018 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)
from spack import *
import os.path
class Snpeff(Package):
"""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/"
url = "https://kent.dl.sourceforge.net/project/snpeff/snpEff_latest_core.zip"
version('2017-11-24', '1fa84a703580a423e27f1e14a945901c')
depends_on('jdk', type=('build', 'run'))
def install(self, spec, prefix):
install_tree('snpEff', 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__), "snpEff.sh")
script = prefix.bin.snpEff
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 = {'backup': False}
filter_file('^java', java, script, **kwargs)
filter_file('snpEff.jar', join_path(prefix.bin, 'snpEff.jar'),
script, **kwargs)
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