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