# 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 GmapGsnap(AutotoolsPackage):
    """GMAP: A Genomic Mapping and Alignment Program for
    mRNA and EST Sequences, and GSNAP: Genomic Short-read
    Nucleotide Alignment Program"""

    homepage = "http://research-pub.gene.com/gmap/"
    url = "http://research-pub.gene.com/gmap/src/gmap-gsnap-2017-06-16.tar.gz"

    maintainers("snehring")

    license("Apache-2.0")

    version(
        "2023-07-20", sha256="19e70eebd9b282d8596721812d071efed188b6d5000627b9948f0486f87fe68f"
    )
    version(
        "2023-06-01", sha256="c7e6f6cf644e6f66f9f5a0811a49da8cc81f095a4bd7b7cef2ab10aa5b314430"
    )
    version(
        "2023-04-28", sha256="6e73fab2e8043ebf735c43fe8460d2abd7c1398d1e796dc5b22ba68717f4160c"
    )
    version(
        "2023-03-24", sha256="eec93a2a693c1bc5bf3026b39522f45e8a8aad6e8b8b4239a94aa17f37600762"
    )
    version(
        "2023-02-17", sha256="d54abb6bc59da46823f5a1a9d94872a6b90468699112a6f375ddc7b91340db06"
    )
    version(
        "2021-03-08", sha256="00de0e945b86bcbda50df94c68a61957f3783e232cce466fcd5f8d3a55398aa2"
    )
    version(
        "2020-06-01", sha256="7917f9f78570943f419445e371f2cc948c6741e73c3cbb063391756f4479d365"
    )
    version(
        "2019-05-12", sha256="3dc1b6ee4f6c049c07bcf4a5aba30eb2d732997241cdcad818dab571719f8008"
    )
    version(
        "2019-02-15", sha256="7e82b9867a1e561b4816fb2f2fb916294077c384c6a88bb94cce39bfe71ab3ac"
    )
    version(
        "2018-07-04", sha256="a9f8c1f0810df65b2a089dc10be79611026f4c95e4681dba98fea3d55d598d24"
    )
    version(
        "2018-03-25", sha256="a65bae6115fc50916ad7425d0b5873b611c002690bf35026bfcfc41ee0c0265a"
    )
    version(
        "2018-02-12", sha256="5dedddab7f08f9924a995332ebc7bdbe2621fcd67021690707c876d865091fcc"
    )
    version(
        "2017-06-16", sha256="2a277a6d45cade849be3bfb7b0f69f61ab79744af821a88eb1d599b32f358f8d"
    )
    version(
        "2014-12-28", sha256="108433f3e3ea89b8117c8bb36d396913225caf1261d46ce6d89709ff1b44025d"
    )

    depends_on("zlib-api")
    depends_on("bzip2")
    depends_on("perl", type="run")

    requires("simd=arm", when="target=aarch64", msg="simd=arm is required when building on arm")

    variant(
        "simd",
        description="CPU support.",
        values=(
            conditional("avx2", "sse42", "avx512", "sse2", when="target=x86_64:"),
            conditional("arm", when="@2023-02-17: target=aarch64:"),
            conditional("avx512", "avx512bw", when="@2023-03-24: target=x86_64:"),
        ),
        multi=True,
        default="avx2",
    )

    def configure(self, spec, prefix):
        configure = Executable("../configure")

        for simd in spec.variants["simd"].value:
            with working_dir(simd, create=True):
                configure("--with-simd-level={0}".format(simd), "--prefix={0}".format(prefix))

    def build(self, spec, prefix):
        for simd in spec.variants["simd"].value:
            with working_dir(simd):
                make()

    def check(self):
        for simd in self.spec.variants["simd"].value:
            with working_dir(simd):
                make("check")

    def install(self, spec, prefix):
        for simd in spec.variants["simd"].value:
            with working_dir(simd):
                make("install")

    def setup_build_environment(self, env):
        env.set("PERL", self.spec["perl"].prefix.bin.perl)