# 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 spack.package import *


class Guidance(MakefilePackage):
    """Guidance: Accurate detection of unreliable alignment regions accounting
    for the uncertainty of multiple parameters."""

    homepage = "http://guidance.tau.ac.il/ver2/"
    url = "http://guidance.tau.ac.il/ver2/guidance.v2.02.tar.gz"

    version("2.02", sha256="825e105dde526759fb5bda1cd539b24db0b90b8b586f26b1df74d9c5abaa7844")

    depends_on("perl", type=("build", "run"))
    depends_on("perl-bioperl", type=("build", "run"))
    depends_on("ruby")
    depends_on("prank")
    depends_on("clustalw")
    depends_on("mafft")
    depends_on("muscle")

    conflicts("%gcc@6.2.0:")

    def edit(self, spec, prefix):
        for dir in "Guidance", "Selecton", "bioSequence_scripts_and_constants":
            with working_dir(join_path("www", dir)):
                files = glob.iglob("*.pl")
                for file in files:
                    perl = FileFilter(file)
                    perl.filter("#!/usr/bin/perl -w", "#!/usr/bin/env perl")

    def install(self, spac, prefix):
        mkdir(prefix.bin)
        install_tree("libs", prefix.bin.libs)
        install_tree("programs", prefix.bin.programs)
        install_tree("www", prefix.bin.www)
        with working_dir(join_path("www", "Guidance")):  # copy without suffix
            install("guidance.pl", join_path(prefix.bin.www.Guidance, "guidance"))

    def setup_run_environment(self, env):
        env.prepend_path("PATH", prefix.bin.www.Guidance)