24c01d57cf
* fix remaining flake8 errors * imports: sort imports everywhere in Spack We enabled import order checking in #23947, but fixing things manually drives people crazy. This used `spack style --fix --all` from #24071 to automatically sort everything in Spack so PR submitters won't have to deal with it. This should go in after #24071, as it assumes we're using `isort`, not `flake8-import-order` to order things. `isort` seems to be more flexible and allows `llnl` mports to be in their own group before `spack` ones, so this seems like a good switch.
44 lines
1.6 KiB
Python
44 lines
1.6 KiB
Python
# Copyright 2013-2021 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 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)
|