51 lines
1.7 KiB
Python
51 lines
1.7 KiB
Python
# Copyright Spack Project Developers. See COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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import os
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from spack.package import *
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class Astral(Package):
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"""ASTRAL is a tool for estimating an unrooted species tree given a set of
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unrooted gene trees."""
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homepage = "https://github.com/smirarab/ASTRAL"
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url = "https://github.com/smirarab/ASTRAL/archive/v4.10.7.tar.gz"
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license("Apache-2.0")
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version("5.7.1", sha256="8aa6fd4324efca325d3dde432517090fac314bea95f407b1dd59977181fec77e")
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version(
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"5.6.1",
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sha256="b49a67c9fe19c0c92a89dc2f1a3928840e698a53054a595c61546ca98448a076",
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url="https://github.com/smirarab/ASTRAL/archive/untagged-697f19dbce69929ece09.tar.gz",
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)
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version("4.10.7", sha256="314b49e0129ec06a7c78a1b60d590259ede6a5e75253407031e108d8048fcc79")
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depends_on("java@11", type=("build", "run"))
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depends_on("zip", type="build")
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depends_on("gmake", type="build")
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def install(self, spec, prefix):
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make = Executable("./make.sh")
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make()
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mkdirp(prefix.bin)
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install_tree("lib", prefix.tools.lib)
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jar_file = f"astral.{self.version}.jar"
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install(jar_file, prefix.tools)
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script_sh = join_path(os.path.dirname(__file__), "astral.sh")
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script = prefix.bin.astral
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install(script_sh, script)
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set_executable(script)
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java = self.spec["java"].prefix.bin.java
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kwargs = {"ignore_absent": False, "backup": False, "string": False}
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filter_file("^java", java, script, **kwargs)
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filter_file("astral.jar", join_path(prefix.tools, jar_file), script, **kwargs)
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def setup_run_environment(self, env):
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env.set("ASTRAL_HOME", self.prefix.tools)
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