# 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 spack.package import *


class FrHit(Package):
    """An efficient algorithm for fragment recruitment for next generation
    sequences against microbial reference genomes."""

    homepage = "http://weizhong-lab.ucsd.edu/frhit"
    url = "http://weizhong-lab.ucsd.edu/frhit/fr-hit-v0.7.1-2013-02-20.tar.gz"

    license("MIT")

    version(
        "0.7.1-2013-02-20",
        sha256="44dcfeb73106529fcefb02c017ec7b95b04b6523a2a57683b2bc905c142e62eb",
    )

    depends_on("perl")
    depends_on("python@2.7:")

    # The patch adds the python interpreter to the beginning of the script
    # allowing it to be run directly without passing the entire path to the
    # script to python.
    patch("binning.patch")

    def install(self, spec, prefix):
        make()

        filter_file(r"#!/bin/env perl", "#!/usr/bin/env perl", "frhit2pairend.pl")
        filter_file(r"#!/bin/env perl", "#!/usr/bin/env perl", "psl2sam.pl")

        mkdirp(prefix.bin)
        install("fr-hit", prefix.bin)
        install("frhit2pairend.pl", prefix.bin)
        install("psl2sam.pl", prefix.bin)
        install("binning-1.1.1/bacteria_gitax.pkl", prefix.bin)
        install("binning-1.1.1/binning.py", prefix.bin)
        install("binning-1.1.1/tax.pkl", prefix.bin)