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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 Polypolish(Package):
"""Polypolish is a tool for polishing genome assemblies with short reads.
Unlike other tools in this category, Polypolish uses SAM files where each
read has been aligned to all possible locations (not just a single best
location). This allows it to repair errors in repeat regions that other
alignment-based polishers cannot fix."""
homepage = "https://github.com/rrwick/Polypolish"
url = "https://github.com/rrwick/Polypolish/archive/refs/tags/v0.5.0.tar.gz"
license("GPL-3.0-or-later")
version("0.5.0", sha256="183156093c03094290951f140010b3aef6222a672bf538e9136914178775fb1f")
depends_on("rust")
depends_on("python@3.6:", type="run")
depends_on("bwa", type="run")
def install(self, spec, prefix):
cargo = which("cargo")
cargo("install", "--root", prefix, "--path", ".")
install("scripts/polypolish_insert_filter.py", prefix.bin)
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