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# Copyright 2013-2024 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.package import *
class Haploview(Package):
"""Haploview is designed to simplify and expedite the process of haplotype
analysis."""
homepage = "https://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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