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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
+
+
+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', 'bd9bbca656fe15ecbe615c4732714bc7')
+
+ 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['jdk'].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)