# Copyright 2013-2023 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 os import symlink

from spack.package import *


class LtrRetriever(Package):
    """LTR_retriever is a highly accurate and sensitive program for
    identification of LTR retrotransposons."""

    homepage = "https://github.com/oushujun/LTR_retriever"
    url = "https://github.com/oushujun/LTR_retriever/archive/v2.8.7.tar.gz"

    maintainers("snehring")

    license("GPL-3.0-only")

    version("2.9.4", sha256="a9f4668113d2d75ab97cd85b456f11b00afd4876848a8ef099622ec0d9e505e7")
    version("2.8.7", sha256="29ca6f699c57b5e964aa0ee6c7d3e1e4cd5362dadd789e5f0e8c82fe0bb29369")

    depends_on("perl", type="run")
    depends_on("blast-plus", type="run")
    depends_on("hmmer@3.1b2:", type="run")
    depends_on("cdhit", type="run")
    depends_on("repeatmasker", type="run")
    depends_on("py-tesorter", type="run", when="@2.9.4:")

    def install(self, spec, prefix):
        filter_file(r"BLAST\+=.*", "BLAST+=%s" % spec["blast-plus"].prefix.bin, "paths")
        filter_file(
            "RepeatMasker=.*", "RepeatMasker=%s" % spec["repeatmasker"].prefix.bin, "paths"
        )
        filter_file("HMMER=.*", "HMMER=%s" % spec["hmmer"].prefix.bin, "paths")
        filter_file("CDHIT=.*", "CDHIT=%s" % spec["cdhit"].prefix.bin, "paths")
        filter_file("BLAST=.*", "", "paths")
        if spec.satisfies("@2.9.4:"):
            filter_file(
                "^TEsorter=.*$", "TEsorter={}".format(spec["py-tesorter"].prefix.bin), "paths"
            )

        mkdirp(prefix.opt)
        mkdirp(prefix.bin)

        install_tree(".", prefix.opt.ltr_retriever)

        symlink(prefix.opt.ltr_retriever.LTR_retriever, prefix.bin.LTR_retriever)