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py-panaroo, py-edlib, and py-intbitset: new packages (#31452)

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Luke Diorio-Toth 2022-07-07 19:13:39 -05:00 committed by GitHub
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commit ec7513c8b5
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var/spack/repos/builtin/packages/py-edlib/package.py Normal file
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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 PyEdlib(PythonPackage):
"""Lightweight, super fast library for sequence
alignment using edit (Levenshtein) distance."""
homepage = "https://pypi.org/project/edlib/"
pypi = "edlib/edlib-1.3.9.tar.gz"
version('1.3.9', sha256='64c3dfab3ebe3e759565a0cc71eb4df23cf3ce1713fd558af3c473dddc2a3766')
depends_on('py-setuptools', type='build')

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var/spack/repos/builtin/packages/py-intbitset/package.py Normal file
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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 PyIntbitset(PythonPackage):
"""The intbitset library provides a set implementation to store sorted
unsigned integers either 32-bits integers or an infinite range with fast
set operations implemented via bit vectors in a Python C extension for
speed and reduced memory usage."""
homepage = "https://github.com/inveniosoftware/intbitset"
pypi = "intbitset/intbitset-3.0.1.tar.gz"
version('3.0.1', sha256='f1e6d03c6729922a223c51849df65b9e916e625aefb911784e7f9acd4c207d53')
depends_on('py-setuptools', type='build')

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var/spack/repos/builtin/packages/py-panaroo/package.py Normal file
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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 PyPanaroo(PythonPackage):
"""A Bacterial Pangenome Analysis Pipeline"""
homepage = "https://gtonkinhill.github.io/panaroo"
url = "https://github.com/gtonkinhill/panaroo/archive/refs/tags/v1.2.10.tar.gz"
version('1.2.10', sha256='066e5cd96b59918fa4fcd2dc12c92a273457ee17e2fe55576657c793566e948e')
depends_on('python@3.6.0:', type=('build', 'run'))
depends_on('py-setuptools', type='build')
depends_on('py-biopython', type=('build', 'run'))
depends_on('py-numpy', type=('build', 'run'))
depends_on('py-scipy', type=('build', 'run'))
depends_on('py-matplotlib', type=('build', 'run'))
depends_on('py-plotly', type=('build', 'run'))
depends_on('py-dendropy', type=('build', 'run'))
depends_on('py-scikit-learn', type=('build', 'run'))
depends_on('py-networkx', type=('build', 'run'))
depends_on('py-gffutils', type=('build', 'run'))
depends_on('py-edlib', type=('build', 'run'))
depends_on('py-joblib', type=('build', 'run'))
depends_on('py-tqdm', type=('build', 'run'))
depends_on('py-intbitset', type=('build', 'run'))
depends_on('cdhit', type=('build', 'run'))
depends_on('prokka', type=('build', 'run'))
depends_on('prank', type=('build', 'run'))
depends_on('mafft', type=('build', 'run'))
depends_on('clustal-omega', type=('build', 'run'))
depends_on('mash', type=('build', 'run'))