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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
from spack.package import *
class Genomefinisher(Package):
"""GFinisher is an application tools for refinement and finalization of
prokaryotic genomes assemblies using the bias of GC Skew to identify
assembly errors and organizes the contigs/scaffolds with genomes
references."""
homepage = "http://gfinisher.sourceforge.net"
url = "https://sourceforge.net/projects/gfinisher/files/GenomeFinisher_1.4.zip"
version("1.4", sha256="8efbebaab4b577c72193f14c2c362b96fb949981fd66d2cca1364839af8bf1e3")
depends_on("java@8:", type="run")
def install(self, spec, prefix):
mkdirp(prefix.bin)
jar_file = "GenomeFinisher.jar"
install(jar_file, prefix.bin)
install_tree("lib", prefix.lib)
# 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__), "genomefinisher.sh")
script = prefix.bin.genomefinisher
install(script_sh, script)
set_executable(script)
# Munge the helper script to explicitly point to java and the jar file
# jar file.
java = spec["java"].prefix.bin.java
kwargs = {"ignore_absent": False, "backup": False, "string": False}
filter_file("^java", java, script, **kwargs)
filter_file(jar_file, join_path(prefix.bin, jar_file), script, **kwargs)
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