30 lines
1.1 KiB
Python
30 lines
1.1 KiB
Python
# Copyright 2013-2022 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 Polypolish(Package):
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"""Polypolish is a tool for polishing genome assemblies with short reads.
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Unlike other tools in this category, Polypolish uses SAM files where each
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read has been aligned to all possible locations (not just a single best
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location). This allows it to repair errors in repeat regions that other
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alignment-based polishers cannot fix."""
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homepage = "https://github.com/rrwick/Polypolish"
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url = "https://github.com/rrwick/Polypolish/archive/refs/tags/v0.5.0.tar.gz"
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version("0.5.0", sha256="183156093c03094290951f140010b3aef6222a672bf538e9136914178775fb1f")
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depends_on("rust")
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depends_on("python@3.6:", type="run")
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depends_on("bwa", type="run")
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def install(self, spec, prefix):
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cargo = which("cargo")
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cargo("install", "--root", prefix, "--path", ".")
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install("scripts/polypolish_insert_filter.py", prefix.bin)
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