# 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 Plink(Package):
    """PLINK is a free, open-source whole genome association analysis toolset,
    designed to perform a range of basic, large-scale analyses in a
    computationally efficient manner."""

    homepage = "https://www.cog-genomics.org/plink/1.9/"

    version(
        "1.9-beta6.27",
        commit="a2ea957c893fbb0558358edef27f3ecbf3d360f8",
        git="https://github.com/chrchang/plink-ng.git",
    )
    version(
        "1.9-beta6.10",
        sha256="f8438656996c55a5edd95c223cce96277de6efaab1b9b1d457bfee0c272058d8",
        url="https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20190617.zip",
    )
    version(
        "1.9-beta5",
        sha256="e00ef16ac5abeb6b4c4d77846bd655fafc62669fbebf8cd2e941f07b3111907e",
        url="https://github.com/chrchang/plink-ng/archive/b15c19f.tar.gz",
    )
    version(
        "1.07",
        sha256="70c52ee47eed854293832639dbabb41c7c036db3a4881c136e6a71ecff4ac7f4",
        url="https://zzz.bwh.harvard.edu/plink/dist/plink-1.07-x86_64.zip",
        preferred=True,
    )

    depends_on("atlas", when="@1.9-beta5:1.9-beta6.10")
    depends_on("netlib-lapack", when="@1.9-beta5:1.9-beta6.10")

    with when("@1.9-beta-6.27:"):
        depends_on("zlib-api", when="@1.9-beta6.27:")
        depends_on("blas", when="@1.9-beta6.27:")
        depends_on("lapack", when="@1.9-beta6.27:")

    patch("dynamic_zlib.patch", when="@1.9-beta6.27:")

    def install(self, spec, prefix):
        mkdirp(prefix.bin)
        if spec.version == Version("1.07"):
            install("plink", prefix.bin)
            install("gPLINK.jar", prefix.bin)
        if spec.version == Version("1.9-beta5"):
            with working_dir("1.9"):
                first_compile = Executable("./plink_first_compile")
                first_compile()
                install("plink", prefix.bin)
        if spec.version == Version("1.9-beta6.10"):
            install("plink", prefix.bin)

    @when("@1.9-beta6.27:")
    def setup_build_environment(self, env):
        env.set("BLASFLAGS", self.spec["blas"].libs.ld_flags)
        env.set("ZLIB", self.spec["zlib-api"].libs.ld_flags)

    @when("@1.9-beta6.27:")
    def install(self, spec, prefix):
        with working_dir("1.9"):
            make()
            mkdir(prefix.bin)
            install("plink", prefix.bin)