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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
from spack.package import *
class Igvtools(Package):
"""IGVTools suite of command-line utilities for preprocessing data
files"""
homepage = "https://software.broadinstitute.org/software/igv/home"
url = "https://data.broadinstitute.org/igv/projects/downloads/2.3/igvtools_2.3.98.zip"
version("2.3.98", sha256="07027c179f25960bab9919f255c0f8e08f0861861ac6dc02d92be8313e0316a4")
depends_on("java@8:")
def install(self, spec, prefix):
mkdirp(prefix.bin)
jar_file = "igvtools.jar"
install(jar_file, prefix.bin)
install_tree("genomes", prefix.genomes)
# 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__), "igvtools.sh")
script = prefix.bin.igvtools
install(script_sh, script)
set_executable(script)
# Munge the helper script to explicitly point to java and the
# 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)
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