# 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)

import glob
import os

from spack.package import *


class Kraken2(Package):
    """Kraken2 is a system for assigning taxonomic labels to short DNA
    sequences, usually obtained through metagenomic studies."""

    homepage = "https://ccb.jhu.edu/software/kraken2/"
    url = "https://github.com/DerrickWood/kraken2/archive/v2.1.1.tar.gz"

    maintainers("rberg2")

    license("MIT")

    version("2.1.2", sha256="e5f431e8bc3d5493a79e1d8125f4aacbad24f9ea2cc9657b66da06a32bef6ff3")
    version("2.1.1", sha256="8f3e928cdb32b9e8e6f55b44703d1557b2a5fc3f30f63e8d16e465e19a81dee4")
    version(
        "2.0.8-beta", sha256="f2a91fc57a40b3e87df8ac2ea7c0ff1060cc9295c95de417ee53249ee3f7ad8e"
    )
    version(
        "2.0.7-beta", sha256="baa160f5aef73327e1a79e6d1c54b64b2fcdaee0be31b456f7bc411d1897a744"
    )
    version(
        "2.0.6-beta", sha256="d77db6251179c4d7e16bc9b5e5e9043d25acf81f3e32ad6eadfba829a31e1d09"
    )

    depends_on("perl", type=("build", "run"))
    depends_on("rsync", type=("run"))
    depends_on("wget", type=("run"))

    def install(self, spec, prefix):
        installer = Executable("./install_kraken2.sh")
        installer(self.stage.source_path)
        mkdirp(prefix.bin)
        files = glob.iglob("*")
        for file in files:
            if os.path.isfile(file):
                install(file, prefix.bin)