# 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 os
import shutil

from spack.package import *


class Orthofinder(Package):
    """OrthoFinder is a fast, accurate and comprehensive analysis tool for
    comparative genomics.

    It finds orthologues and orthogroups infers rooted  gene trees for all
    orthogroups and infers a rooted species tree for the species being
    analysed. OrthoFinder also provides comprehensive statistics for
    comparative genomic analyses. OrthoFinder is simple to use and all you
    need to run it is a set of protein sequence files (one per species)
    in FASTA format."""

    homepage = "https://github.com/davidemms/OrthoFinder"
    url = "https://github.com/davidemms/OrthoFinder/releases/download/2.5.2/OrthoFinder_source.tar.gz"

    license("GPL-3.0-or-later")

    version("2.5.5", sha256="43d034a66a13adba8872a0d4a76e32c25305a7fae638754adb61c37a3f957bd9")
    version("2.5.4", sha256="a735c81999e8e3026ad62536b14e5b0391c9fc632f872f99857936ac60003ba5")
    version("2.5.2", sha256="e0752b66866e23a11f0592e880fac5f67258f9cf926f926dec8849564c41b8f7")
    version("2.2.0", sha256="375f711086b44e2118d7d460821294744245e254e5fa2151dfe73100c0707a8c")

    variant("blast", default=False, description="Enable BLAST+ local alignment", when="@2.3.1:")
    variant("mmseqs2", default=False, description="Enable MMseqs2 local alignment", when="@2.2.7:")
    variant("muscle", default=False, description="Enable multiple sequence alignment with muscle")
    variant(
        "iqtree", default=False, description="Enable tree building with IQ-TREE", when="@2.3.7:"
    )
    variant("raxml", default=False, description="Enable tree building with RAxML")
    variant(
        "raxml-ng", default=False, description="Enable tree building with RAxML-NG", when="@2.2.7:"
    )

    # general dependencies
    depends_on("py-numpy", type="run")
    depends_on("py-scipy", type="run")
    depends_on("diamond", type="run")
    depends_on("blast-plus", type="run", when="@:2.2.7")
    depends_on("mcl", type="run")
    depends_on("fastme", type="run")
    depends_on("mafft", type="run")
    depends_on("fasttree", type="run")
    # variant dependencies
    depends_on("blast-plus", type="run", when="+blast")
    depends_on("mmseqs2", type="run", when="+mmseqs2")
    depends_on("muscle5", type="run", when="+muscle")
    depends_on("iqtree2", type="run", when="+iqtree")
    depends_on("raxml", type="run", when="+raxml")
    depends_on("raxml-ng", type="run", when="+raxml-ng")

    def url_for_version(self, version):
        if "@:2.3.6" in self.spec:
            url = "https://github.com/davidemms/OrthoFinder/releases/download/{0}/OrthoFinder-{0}_source.tar.gz"
            return url.format(version)
        else:
            url = "https://github.com/davidemms/OrthoFinder/releases/download/{0}/OrthoFinder_source.tar.gz"
            return url.format(version)

    def install(self, spec, prefix):
        if "@2.2.0" in spec:
            install_tree("./orthofinder", prefix.bin)
        else:
            install_tree(".", prefix.bin)
            shutil.rmtree(prefix.bin.scripts_of.bin)
        os.rename("%s/orthofinder.py" % prefix.bin, "%s/orthofinder" % prefix.bin)

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