# 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 Portcullis(AutotoolsPackage):
    """PORTable CULLing of Invalid Splice junctions"""

    homepage = "https://github.com/EI-CoreBioinformatics/portcullis"
    url = "https://github.com/EI-CoreBioinformatics/portcullis/archive/refs/tags/Release-1.1.2.tar.gz"

    license("GPL-3.0-only")

    version("1.2.3", sha256="172452b5cef12a8dcc2c1c68527000743114136ee63a0dbe307ac4e2a816bc99")
    version("1.1.2", sha256="5c581a7f827ffeecfe68107b7fe27ed60108325fd2f86a79d93f61b328687749")

    depends_on("autoconf@2.53:", type="build")
    depends_on("automake@1.11:", type="build")
    depends_on("libtool@2.4.2:", type="build")
    depends_on("boost")
    depends_on("m4", type="build")

    depends_on("zlib-api", type="build")
    depends_on("samtools", type="build")

    depends_on("python@3.4:", type=("build", "run"))
    depends_on("py-setuptools", type=("build", "run"))
    depends_on("py-pandas", type=("build", "run"))

    # later versions of py-sphinx don't get detected by the configure script
    depends_on("py-sphinx@1.3:1.4")

    def patch(self):
        # remove static linking to libstdc++
        filter_file('AM_LDFLAGS="-static-libstdc++"', 'AM_LDFLAGS=""', "configure.ac", string=True)

        # prevent install scripts from ruining our PYTHONPATH
        filter_file(
            "export PYTHONPATH=$(DESTDIR)$(pythondir)",
            'export PYTHONPATH="$(PYTHONPATH):$(DESTDIR)$(pythondir)"',
            "scripts/Makefile.am",
            string=True,
        )

        # remove -m64 on aarch64
        if self.spec.target.family == "aarch64":
            for f in ["lib/Makefile.am", "src/Makefile.am"]:
                filter_file("-m64", "", f)

    def build(self, spec, prefix):
        # build manpages
        make("man")