# 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
from os import chmod

from spack.package import *


class Mirdeep2(Package):
    """miRDeep2 is a completely overhauled tool which discovers microRNA genes
    by analyzing sequenced RNAs."""

    homepage = "https://www.mdc-berlin.de/8551903/en/"
    url = "https://www.mdc-berlin.de/system/files/migrated_files/fiona/mirdeep2_0_0_8.zip"

    version("0.0.8", sha256="eeb24ee1b0e76b49ee2f542da3ee7d46d163c80b152709e963492b79f4fca1b8")

    depends_on("perl", type=("build", "run"))
    depends_on("perl-pdf-api2", type=("build", "run"))
    depends_on("bowtie")
    depends_on("viennarna")
    depends_on("squid")
    depends_on("randfold")

    def url_for_version(self, version):
        url = "https://www.mdc-berlin.de/system/files/migrated_files/fiona/mirdeep2_{0}.zip"
        return url.format(version.underscored)

    def patch(self):
        with working_dir("src"):
            files = glob.iglob("*.pl")
            for file in files:
                chmod(file, 0o755)
                change = FileFilter(file)
                change.filter("usr/bin/perl", "usr/bin/env perl")
                change.filter("perl -W", "perl")
                change.filter("../Rfam_for_miRDeep.fa", "Rfam_for_miRDeep.fa")
                change.filter("../install_successful", "install_successful")

    def install(self, spec, prefix):
        install_tree("src", prefix.bin)
        install("Rfam_for_miRDeep.fa", prefix.bin)
        # miRDeep looks for the install_sucessful file to check if you used
        # their automated install script which we'll just be kind of hacking
        # around
        touch(prefix.bin.install_successful)