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# Copyright 2013-2023 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 Varscan(Package):
"""Variant calling and somatic mutation/CNV detection for next-generation
sequencing data"""
homepage = "https://dkoboldt.github.io/varscan/"
url = "https://github.com/dkoboldt/varscan/releases/download/2.4.2/VarScan.v2.4.2.jar"
version(
"2.4.2",
sha256="34ff6462f91fb6ed3f11e867ab4a179efae5dd8214b97fa261fc616f23d4d031",
expand=False,
)
depends_on("java", type=("build", "run"))
def install(self, spec, prefix):
mkdirp(prefix.bin)
mkdirp(prefix.jar)
jar_file = "VarScan.v{v}.jar".format(v=self.version.dotted)
install(jar_file, prefix.jar)
script_sh = join_path(os.path.dirname(__file__), "varscan.sh")
script = prefix.bin.varscan
install(script_sh, script)
set_executable(script)
java = join_path(self.spec["java"].prefix, "bin", "java")
kwargs = {"ignore_absent": False, "backup": False, "string": False}
filter_file("^java", java, script, **kwargs)
filter_file("varscan.jar", join_path(prefix.jar, jar_file), script, **kwargs)
def setup_run_environment(self, env):
env.set("VARSCAN_HOME", self.prefix.jar)
env.set("CLASSPATH", self.prefix.jar)
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