# 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 Tophat(AutotoolsPackage):
    """Spliced read mapper for RNA-Seq."""

    homepage = "https://ccb.jhu.edu/software/tophat/index.shtml"
    url = "https://github.com/infphilo/tophat/archive/v2.1.1.tar.gz"

    license("BSL-1.0")

    version("2.1.2", sha256="15016b82255dad085d4ee7d970e50f0e53a280d466335553d47790d8344ff4b1")
    version("2.1.1", sha256="991b1b7c840a5f5c4e9a15b2815983257d2b0748246af0b9094c7d07552b023e")

    depends_on("autoconf", type="build")
    # 2.1.1 only builds with automake@1.15.1.  There's a patch here:
    # https://github.com/spack/spack/pull/8244, which was incorporated
    # upstream in 2.1.2, which is known to build with 1.16.1 and 1.15.1.
    depends_on("automake", type="build")
    depends_on("automake@1.15.1", when="@:2.1.1", type="build")
    depends_on("libtool", type="build")
    depends_on("m4", type="build")

    depends_on("boost@1.47:+exception+chrono+system+random+atomic+thread")
    depends_on("bowtie2", type="run")

    parallel = False

    def patch(self):
        # Newer versions of autoconf hate calling AM_INIT_AUTOMAKE twice
        filter_file(r"^AM_INIT_AUTOMAKE$", "", "configure.ac")

    def setup_build_environment(self, env):
        env.append_flags("CFLAGS", self.compiler.cxx98_flag)

    def configure_args(self):
        return ["--with-boost={0}".format(self.spec["boost"].prefix)]