# 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 Eagle(MakefilePackage):
    """EAGLE: Explicit Alternative Genome Likelihood Evaluator"""

    homepage = "https://github.com/tony-kuo/eagle"
    url = "https://github.com/tony-kuo/eagle/archive/v1.1.2.tar.gz"
    maintainers("snehring")

    license("GPL-3.0-only")

    version("1.1.3", sha256="bd510b8eef2de14898cbf417e1c7a30b97ddaba24e5e2834da7b02767362fe3c")
    version("1.1.2", sha256="afe967560d1f8fdbd0caf4b93b5f2a86830e9e4d399fee4a526140431343045e")

    depends_on("curl")
    depends_on("zlib-api")
    depends_on("lzma")
    depends_on("htslib")

    def edit(self, spec, prefix):
        # remove unused gcc flags
        filter_file("$(LFLAGS) $(INCLUDES)", "", "Makefile", string=True)

        # drop static link to htslib
        filter_file("$(LIBS)", "", "Makefile", string=True)

        # don't try to build htslib.
        filter_file("all: UTIL HTSLIB", "all: UTIL", "Makefile", string=True)

        # add htslib link to ldflags
        filter_file("-lcurl", "-lcurl -lhts", "Makefile", string=True)

        # use spack C compiler
        filter_file("CC=.*", "CC={0}".format(spack_cc), "Makefile")

        # let the user inject march if they want
        filter_file("-march=native", "", "Makefile", string=True)

    def install(self, spec, prefix):
        mkdirp(prefix.bin)

        bins = ["eagle", "eagle-rc", "eagle-nm"]

        for b in bins:
            install(b, prefix.bin)