# 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)

from spack.package import *


class Vegas2(Package):
    """ "VEGAS2 is an extension that uses 1,000 Genomes data to model SNP
    correlations across the autosomes and chromosome X"""

    homepage = "https://vegas2.qimrberghofer.edu.au/"
    url = "https://vegas2.qimrberghofer.edu.au/vegas2v2"

    version(
        "2",
        sha256="dc85834219141a4e9a246391b48185a739223a5e00b1b1c4d2517822388278ba",
        expand=False,
    )

    depends_on("perl", type="run")
    depends_on("r", type="run")
    depends_on("plink")
    depends_on("r-mvtnorm", type="run")
    depends_on("r-corpcor", type="run")

    def url_for_version(self, version):
        url = "https://vegas2.qimrberghofer.edu.au/vegas2v{0}"
        return url.format(version)

    def install(self, spec, prefix):
        mkdirp(prefix.bin)
        install("vegas2v{0}".format(self.version), prefix.bin)