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# 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")
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