# 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 Mummer(Package):
    """MUMmer is a system for rapidly aligning entire genomes."""

    homepage = "http://mummer.sourceforge.net/"
    url = "https://sourceforge.net/projects/mummer/files/mummer/3.23/MUMmer3.23.tar.gz/download"

    license("Artistic-1.0")

    version("3.23", sha256="1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f")

    depends_on("gnuplot")
    depends_on("perl", type=("build", "run"))

    patch("Makefile.patch")
    patch("scripts-Makefile.patch")

    def patch(self):
        """Fix mummerplot's use of defined on hashes (deprecated
        since perl@5.10, made illegal in perl@5.20."""

        kwargs = {"string": True}
        filter_file("defined (%", "(%", "scripts/mummerplot.pl", **kwargs)

    def install(self, spec, prefix):
        if self.run_tests:
            make("check")
        make("INSTALL_TOP_DIR={0}".format(prefix))
        bd = prefix.bin
        abd = join_path(prefix, "aux_bin")
        sd = join_path(prefix, "scripts")
        mkdirp(bd)
        mkdirp(abd)
        mkdirp(sd)

        bins = [
            "show-tiling",
            "show-snps",
            "show-coords",
            "show-aligns",
            "show-diff",
            "delta-filter",
            "combineMUMs",
            "mummer",
            "repeat-match",
            "annotate",
            "mgaps",
            "gaps",
            "dnadiff",
            "nucmer2xfig",
            "run-mummer3",
            "mummerplot",
            "promer",
            "run-mummer1",
            "nucmer",
            "mapview",
            "exact-tandems",
        ]
        aux_bins = ["aux_bin/postnuc", "aux_bin/postpro", "aux_bin/prenuc", "aux_bin/prepro"]
        scripts = ["scripts/Foundation.pm"]

        for f in bins:
            install(f, join_path(bd, f))
        for f in aux_bins:
            install(f, join_path(abd, f[8:]))
        for f in scripts:
            install(f, join_path(sd, f[8:]))