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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 Astral(Package):
"""ASTRAL is a tool for estimating an unrooted species tree given a set of
unrooted gene trees."""
homepage = "https://github.com/smirarab/ASTRAL"
url = "https://github.com/smirarab/ASTRAL/archive/v4.10.7.tar.gz"
license("Apache-2.0")
version("5.7.1", sha256="8aa6fd4324efca325d3dde432517090fac314bea95f407b1dd59977181fec77e")
version(
"5.6.1",
sha256="b49a67c9fe19c0c92a89dc2f1a3928840e698a53054a595c61546ca98448a076",
url="https://github.com/smirarab/ASTRAL/archive/untagged-697f19dbce69929ece09.tar.gz",
)
version("4.10.7", sha256="314b49e0129ec06a7c78a1b60d590259ede6a5e75253407031e108d8048fcc79")
depends_on("java", type=("build", "run"))
depends_on("zip", type="build")
def install(self, spec, prefix):
make = Executable("./make.sh")
make()
mkdirp(prefix.bin)
install_tree("lib", prefix.tools.lib)
jar_file = f"astral.{self.version}.jar"
install(jar_file, prefix.tools)
script_sh = join_path(os.path.dirname(__file__), "astral.sh")
script = prefix.bin.astral
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("astral.jar", join_path(prefix.tools, jar_file), script, **kwargs)
def setup_run_environment(self, env):
env.set("ASTRAL_HOME", self.prefix.tools)
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