# 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 os import symlink

from spack.package import *


class Bridger(MakefilePackage, SourceforgePackage):
    """Bridger : An Efficient De novo Transcriptome Assembler For
    RNA-Seq Data"""

    homepage = "https://sourceforge.net/projects/rnaseqassembly/"
    sourceforge_mirror_path = "rnaseqassembly/Bridger_r2014-12-01.tar.gz"

    license("GPL-2.0-only")

    version(
        "2014-12-01", sha256="8fbec8603ea8ad2162cbd0c658e4e0a4af6453bdb53310b4b7e0d112e40b5737"
    )
    depends_on("boost + exception + filesystem + system + serialization + graph")
    depends_on("ncurses~termlib")
    depends_on("perl", type="run")

    def flag_handler(self, name, flags):
        if name == "cflags":
            # some of the plugins require gnu extensions
            flags.append("-std=gnu99")
        if name == "cxxflags":
            flags.append("-std=c++03")
        return (flags, None, None)

    def install(self, spec, prefix):
        # bridger depends very much on perl scripts/etc in the source tree
        install_path = join_path(prefix, "usr/local/bridger")
        mkdirp(install_path)
        install_tree(".", install_path)

        # symlink the init script to /bin
        mkdirp(prefix.bin)
        symlink(join_path(install_path, "Bridger.pl"), join_path(prefix.bin, "Bridger.pl"))