From ec7513c8b51a2e9ef2443895a95089019b6d768f Mon Sep 17 00:00:00 2001 From: Luke Diorio-Toth Date: Thu, 7 Jul 2022 19:13:39 -0500 Subject: py-panaroo, py-edlib, and py-intbitset: new packages (#31452) --- .../repos/builtin/packages/py-edlib/package.py | 19 +++++++++++ .../repos/builtin/packages/py-intbitset/package.py | 21 ++++++++++++ .../repos/builtin/packages/py-panaroo/package.py | 38 ++++++++++++++++++++++ 3 files changed, 78 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-edlib/package.py create mode 100644 var/spack/repos/builtin/packages/py-intbitset/package.py create mode 100644 var/spack/repos/builtin/packages/py-panaroo/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-edlib/package.py b/var/spack/repos/builtin/packages/py-edlib/package.py new file mode 100644 index 0000000000..991b82b799 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-edlib/package.py @@ -0,0 +1,19 @@ +# 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') diff --git a/var/spack/repos/builtin/packages/py-intbitset/package.py b/var/spack/repos/builtin/packages/py-intbitset/package.py new file mode 100644 index 0000000000..0c3049bd66 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-intbitset/package.py @@ -0,0 +1,21 @@ +# 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') diff --git a/var/spack/repos/builtin/packages/py-panaroo/package.py b/var/spack/repos/builtin/packages/py-panaroo/package.py new file mode 100644 index 0000000000..9e3c2f455a --- /dev/null +++ b/var/spack/repos/builtin/packages/py-panaroo/package.py @@ -0,0 +1,38 @@ +# 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')) -- cgit v1.2.3-70-g09d2