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# 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.path
from spack import *
class Haploview(Package):
"""Haploview is designed to simplify and expedite the process of haplotype
analysis."""
homepage = "http://www.broadinstitute.org/haploview/haploview"
url = "https://downloads.sourceforge.net/project/haploview/release/Haploview4.1.jar"
version('4.1', sha256='b3ffe4c3d8bbab6af5eebf89a2dccdb185280088f70ae84c84be60f85f10201d', expand=False)
depends_on('java', type=('build', 'run'))
def install(self, spec, prefix):
mkdirp(prefix.bin)
jar_file = 'Haploview{v}.jar'.format(v=self.version)
install(jar_file, prefix.bin)
script_sh = join_path(os.path.dirname(__file__), "haploview.sh")
script = prefix.bin.haploview
install(script_sh, script)
set_executable(script)
java = self.spec['java'].prefix.bin.java
kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
filter_file('^java', java, script, **kwargs)
filter_file('haploview.jar', join_path(prefix.bin, jar_file),
script, **kwargs)
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