# 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)


from spack.package import *


class Vardictjava(Package):
    """VarDictJava is a variant discovery program written in Java.
    It is a partial Java port of VarDict variant caller."""

    homepage = "https://github.com/AstraZeneca-NGS/VarDictJava"
    url = (
        "https://github.com/AstraZeneca-NGS/VarDictJava/releases/download/v1.5.1/VarDict-1.5.1.tar"
    )

    version("1.5.1", sha256="f1d710d238e8ab41b02a99fa8698baeee8c8668635a847b826913dd03a9176b9")

    depends_on("java@8:", type="run")

    def install(self, spec, prefix):
        mkdirp(prefix.bin)
        install("bin/VarDict", prefix.bin)

        mkdirp(prefix.lib)
        install("lib/*.jar", prefix.lib)