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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 Pgdspider(Package):
""" "PGDSpider is a powerful automated data conversion tool for population
genetic and genomics programs"""
homepage = "http://www.cmpg.unibe.ch/software/PGDSpider"
url = "http://www.cmpg.unibe.ch/software/PGDSpider/PGDSpider_2.1.1.2.zip"
license("BSD-3-Clause")
version("2.1.1.5", sha256="8564427caf1f5c6200ba8f22a2bc2ef0fa87ae7c6571e4df3b8438cc00fa121c")
version("2.1.1.2", sha256="a630ef9f3ef0c36be0d613867c5293378d77b52396ac701bc7b9ec5d3ba7f2e1")
depends_on("java", type=("build", "run"))
depends_on("bcftools")
depends_on("bwa")
depends_on("samtools")
def install(self, spec, prefix):
mkdirp(prefix.bin)
jar_file = "PGDSpider{0}-cli.jar".format(self.version.up_to(1))
install(jar_file, prefix.bin)
script_sh = join_path(os.path.dirname(__file__), "pgdspider.sh")
script = prefix.bin.pgdspider
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("pgdspider.jar", join_path(prefix.bin, jar_file), script, **kwargs)
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