e51748ee8f
Introduces a new virtual zlib-api, which replaces zlib in most packages. This allows users to switch to zlib-ng by default for better performance.
55 lines
1.9 KiB
Python
55 lines
1.9 KiB
Python
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class Portcullis(AutotoolsPackage):
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"""PORTable CULLing of Invalid Splice junctions"""
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homepage = "https://github.com/EI-CoreBioinformatics/portcullis"
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url = "https://github.com/EI-CoreBioinformatics/portcullis/archive/refs/tags/Release-1.1.2.tar.gz"
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version("1.2.3", sha256="172452b5cef12a8dcc2c1c68527000743114136ee63a0dbe307ac4e2a816bc99")
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version("1.1.2", sha256="5c581a7f827ffeecfe68107b7fe27ed60108325fd2f86a79d93f61b328687749")
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depends_on("autoconf@2.53:", type="build")
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depends_on("automake@1.11:", type="build")
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depends_on("libtool@2.4.2:", type="build")
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depends_on("boost")
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depends_on("m4", type="build")
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depends_on("zlib-api", type="build")
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depends_on("samtools", type="build")
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depends_on("python@3.4:", type=("build", "run"))
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depends_on("py-setuptools", type=("build", "run"))
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depends_on("py-pandas", type=("build", "run"))
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# later versions of py-sphinx don't get detected by the configure script
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depends_on("py-sphinx@1.3:1.4")
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def patch(self):
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# remove static linking to libstdc++
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filter_file('AM_LDFLAGS="-static-libstdc++"', 'AM_LDFLAGS=""', "configure.ac", string=True)
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# prevent install scripts from ruining our PYTHONPATH
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filter_file(
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"export PYTHONPATH=$(DESTDIR)$(pythondir)",
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'export PYTHONPATH="$(PYTHONPATH):$(DESTDIR)$(pythondir)"',
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"scripts/Makefile.am",
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string=True,
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)
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# remove -m64 on aarch64
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if self.spec.target.family == "aarch64":
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for f in ["lib/Makefile.am", "src/Makefile.am"]:
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filter_file("-m64", "", f)
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def build(self, spec, prefix):
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# build manpages
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make("man")
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