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Diffstat (limited to 'var/spack/repos/builtin/packages/genomefinisher/package.py')
-rw-r--r-- | var/spack/repos/builtin/packages/genomefinisher/package.py | 42 |
1 files changed, 42 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/genomefinisher/package.py b/var/spack/repos/builtin/packages/genomefinisher/package.py new file mode 100644 index 0000000000..d9030c2a19 --- /dev/null +++ b/var/spack/repos/builtin/packages/genomefinisher/package.py @@ -0,0 +1,42 @@ +# 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) |