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# Copyright 2013-2022 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 PyUnicycler(PythonPackage):
"""Unicycler is an assembly pipeline for bacterial genomes. It can
assemble Illumina-only read sets where it functions as a SPAdes-optimiser.
It can also assembly long-read-only sets (PacBio or Nanopore) where it
runs a miniasm+Racon pipeline. For the best possible assemblies, give it
both Illumina reads and long reads, and it will conduct a hybrid assembly.
"""
homepage = "https://github.com/rrwick/Unicycler"
url = "https://github.com/rrwick/Unicycler/archive/v0.4.5.tar.gz"
version('0.5.0', sha256='84a8709c9f2e624225410af702d779ffb0cb06f7c22c20e1f01b989945e08a47')
version('0.4.9', sha256='84bea8f3e8f99a1e63e5230ffe474a696db8caa67569c3a96ae12906d32a35eb')
version('0.4.8', sha256='e948871e4de9db5964c9ca6f8f877c3cbe6a46f62052dfab52ffe0f45bbbd203')
version('0.4.7', sha256='a8cf65e46dc2694b0fbd4e9190c73a1f300921457aadfab27a1792b785620d63')
version('0.4.6', sha256='56f6f358a5d1f8dd0fcd1df04504079fc42cec8453a36ee59ff89295535d03f5')
version('0.4.5', sha256='67043656b31a4809f8fa8f73368580ba7658c8440b9f6d042c7f70b5eb6b19ae')
depends_on('python@3.4:', type=('build', 'link', 'run'))
depends_on('py-setuptools', type=('build', 'run'))
depends_on('racon', type=('build', 'link', 'run'))
depends_on('blast-plus', type='run')
# for version 0.5.0
depends_on('spades@3.14.0:', type='run', when='@0.5.0')
# for versions 0.4.9 and earlier
depends_on('spades@3.6.2:3.13.0', type='run', when='@:0.4.9')
depends_on('pilon', type='run', when='@:0.4.9')
depends_on('java', type=('build', 'run'), when='@:0.4.9')
depends_on('bowtie2', type='run', when='@:0.4.9')
depends_on('samtools@1.0:', type=('build', 'link', 'run'), when='@:0.4.9')
conflicts('%gcc@:4.9.0')
conflicts('%clang@:3.4.2')
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