34 lines
1.2 KiB
Python
34 lines
1.2 KiB
Python
# Copyright 2013-2024 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 PyWhatshap(PythonPackage):
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"""WhatsHap is a software for phasing genomic variants using DNA
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sequencing reads, also called read-based phasing or haplotype
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assembly."""
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homepage = "https://whatshap.readthedocs.io/en/latest/"
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url = "https://bitbucket.org/whatshap/whatshap/get/v0.17.tar.gz"
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license("MIT")
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version("0.17", sha256="5f342cbd28f5d3e79490754f067aa67e8bb059da1c042d944b9f75663ef6b055")
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depends_on("python@3.4:", type=("build", "run"))
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depends_on("py-setuptools", type="build")
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depends_on("py-cython@0.17:", type=("build", "run"))
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depends_on("py-pysam@0.14.0:", type="run")
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depends_on("py-xopen", type="run")
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depends_on("py-pyvcf", type="run")
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depends_on("py-pyfaidx", type="run")
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depends_on("py-networkx", type="run")
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def patch(self):
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# there is a stray \xe2 somewhere in setup.py,
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# explicitly using utf-8 will let the install proceed
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filter_file('^"""$', '#coding: utf-8\n"""', "setup.py")
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