%global _empty_manifest_terminate_build 0 Name: python-nextstrain-augur Version: 22.0.0 Release: 1 Summary: A bioinformatics toolkit for phylogenetic analysis License: GNU Affero General Public License v3 URL: https://github.com/nextstrain/augur Source0: https://mirrors.nju.edu.cn/pypi/web/packages/3c/b2/86b50f68dcc8bb281fdf1c413f6a9ba098c7ee3f0f921f45be008887418c/nextstrain-augur-22.0.0.tar.gz BuildArch: noarch Requires: python3-bcbio-gff Requires: python3-biopython Requires: python3-cvxopt Requires: python3-isodate Requires: python3-jsonschema Requires: python3-networkx Requires: python3-numpy Requires: python3-packaging Requires: python3-pandas Requires: python3-phylo-treetime Requires: python3-pyfastx Requires: python3-scipy Requires: python3-xopen[zstd] Requires: python3-cram Requires: python3-deepdiff Requires: python3-freezegun Requires: python3-nextstrain-sphinx-theme Requires: python3-pylint Requires: python3-pytest Requires: python3-pytest-cov Requires: python3-pytest-mock Requires: python3-recommonmark Requires: python3-snakemake Requires: python3-Sphinx Requires: python3-sphinx-autobuild Requires: python3-sphinx-argparse Requires: python3-sphinx-markdown-tables Requires: python3-sphinx-rtd-theme Requires: python3-sphinx-autodoc-typehints Requires: python3-wheel Requires: python3-ipdb %description [![Build Status](https://github.com/nextstrain/augur/actions/workflows/ci.yaml/badge.svg?branch=master)](https://github.com/nextstrain/augur/actions/workflows/ci.yaml) [![PyPI version](https://badge.fury.io/py/nextstrain-augur.svg)](https://pypi.org/project/nextstrain-augur/) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/augur/README.html) [![Documentation Status](https://readthedocs.org/projects/nextstrain-augur/badge/?version=latest)](https://docs.nextstrain.org/projects/augur/en/stable/) [![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0) [![DOI](https://joss.theoj.org/papers/10.21105/joss.02906/status.svg)](https://doi.org/10.21105/joss.02906) ## About Nextstrain Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually-updated view of publicly available data with powerful analytics and visualizations showing pathogen evolution and epidemic spread. Our goal is to aid epidemiological understanding and improve outbreak response. Resulting data and inferences are available live at the website [nextstrain.org](https://nextstrain.org). ## About Augur *Definition: One held to foretell events by omens.* Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data. It provides a collection of commands which are designed to be composable into larger processing pipelines. The output of augur is a series of JSONs that can be used to visualize your results using [Auspice](https://github.com/nextstrain/auspice). ## Quickstart [Follow instructions to install Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html). Try out an analysis of real virus data by [completing the Zika tutorial](https://nextstrain.org/docs/tutorials/zika). ## Documentation * [Overview of how Augur fits together with other Nextstrain tools](https://docs.nextstrain.org/en/latest/learn/parts.html) * [Overview of Augur usage](https://docs.nextstrain.org/projects/augur/en/stable/usage/usage.html) * [Technical documentation for Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html) * [Contributor guide](https://github.com/nextstrain/.github/blob/master/CONTRIBUTING.md) * [Developer docs for Augur](./docs/contribute/DEV_DOCS.md) * [Changelog](./CHANGES.md) ## Citation Huddleston J, Hadfield J, Sibley TR, Lee J, Fay K, Ilcisin M, Harkins E, Bedford T, Neher RA, Hodcroft EB, (2021). Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. Journal of Open Source Software, 6(57), 2906, https://doi.org/10.21105/joss.02906 ## License and copyright Copyright 2014-2022 Trevor Bedford and Richard Neher. Source code to Nextstrain is made available under the terms of the [GNU Affero General Public License](LICENSE.txt) (AGPL). Nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. %package -n python3-nextstrain-augur Summary: A bioinformatics toolkit for phylogenetic analysis Provides: python-nextstrain-augur BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-nextstrain-augur [![Build Status](https://github.com/nextstrain/augur/actions/workflows/ci.yaml/badge.svg?branch=master)](https://github.com/nextstrain/augur/actions/workflows/ci.yaml) [![PyPI version](https://badge.fury.io/py/nextstrain-augur.svg)](https://pypi.org/project/nextstrain-augur/) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/augur/README.html) [![Documentation Status](https://readthedocs.org/projects/nextstrain-augur/badge/?version=latest)](https://docs.nextstrain.org/projects/augur/en/stable/) [![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0) [![DOI](https://joss.theoj.org/papers/10.21105/joss.02906/status.svg)](https://doi.org/10.21105/joss.02906) ## About Nextstrain Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually-updated view of publicly available data with powerful analytics and visualizations showing pathogen evolution and epidemic spread. Our goal is to aid epidemiological understanding and improve outbreak response. Resulting data and inferences are available live at the website [nextstrain.org](https://nextstrain.org). ## About Augur *Definition: One held to foretell events by omens.* Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data. It provides a collection of commands which are designed to be composable into larger processing pipelines. The output of augur is a series of JSONs that can be used to visualize your results using [Auspice](https://github.com/nextstrain/auspice). ## Quickstart [Follow instructions to install Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html). Try out an analysis of real virus data by [completing the Zika tutorial](https://nextstrain.org/docs/tutorials/zika). ## Documentation * [Overview of how Augur fits together with other Nextstrain tools](https://docs.nextstrain.org/en/latest/learn/parts.html) * [Overview of Augur usage](https://docs.nextstrain.org/projects/augur/en/stable/usage/usage.html) * [Technical documentation for Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html) * [Contributor guide](https://github.com/nextstrain/.github/blob/master/CONTRIBUTING.md) * [Developer docs for Augur](./docs/contribute/DEV_DOCS.md) * [Changelog](./CHANGES.md) ## Citation Huddleston J, Hadfield J, Sibley TR, Lee J, Fay K, Ilcisin M, Harkins E, Bedford T, Neher RA, Hodcroft EB, (2021). Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. Journal of Open Source Software, 6(57), 2906, https://doi.org/10.21105/joss.02906 ## License and copyright Copyright 2014-2022 Trevor Bedford and Richard Neher. Source code to Nextstrain is made available under the terms of the [GNU Affero General Public License](LICENSE.txt) (AGPL). Nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. %package help Summary: Development documents and examples for nextstrain-augur Provides: python3-nextstrain-augur-doc %description help [![Build Status](https://github.com/nextstrain/augur/actions/workflows/ci.yaml/badge.svg?branch=master)](https://github.com/nextstrain/augur/actions/workflows/ci.yaml) [![PyPI version](https://badge.fury.io/py/nextstrain-augur.svg)](https://pypi.org/project/nextstrain-augur/) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/augur/README.html) [![Documentation Status](https://readthedocs.org/projects/nextstrain-augur/badge/?version=latest)](https://docs.nextstrain.org/projects/augur/en/stable/) [![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0) [![DOI](https://joss.theoj.org/papers/10.21105/joss.02906/status.svg)](https://doi.org/10.21105/joss.02906) ## About Nextstrain Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually-updated view of publicly available data with powerful analytics and visualizations showing pathogen evolution and epidemic spread. Our goal is to aid epidemiological understanding and improve outbreak response. Resulting data and inferences are available live at the website [nextstrain.org](https://nextstrain.org). ## About Augur *Definition: One held to foretell events by omens.* Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data. It provides a collection of commands which are designed to be composable into larger processing pipelines. The output of augur is a series of JSONs that can be used to visualize your results using [Auspice](https://github.com/nextstrain/auspice). ## Quickstart [Follow instructions to install Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html). Try out an analysis of real virus data by [completing the Zika tutorial](https://nextstrain.org/docs/tutorials/zika). ## Documentation * [Overview of how Augur fits together with other Nextstrain tools](https://docs.nextstrain.org/en/latest/learn/parts.html) * [Overview of Augur usage](https://docs.nextstrain.org/projects/augur/en/stable/usage/usage.html) * [Technical documentation for Augur](https://docs.nextstrain.org/projects/augur/en/stable/installation/installation.html) * [Contributor guide](https://github.com/nextstrain/.github/blob/master/CONTRIBUTING.md) * [Developer docs for Augur](./docs/contribute/DEV_DOCS.md) * [Changelog](./CHANGES.md) ## Citation Huddleston J, Hadfield J, Sibley TR, Lee J, Fay K, Ilcisin M, Harkins E, Bedford T, Neher RA, Hodcroft EB, (2021). Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. Journal of Open Source Software, 6(57), 2906, https://doi.org/10.21105/joss.02906 ## License and copyright Copyright 2014-2022 Trevor Bedford and Richard Neher. Source code to Nextstrain is made available under the terms of the [GNU Affero General Public License](LICENSE.txt) (AGPL). Nextstrain is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details. %prep %autosetup -n nextstrain-augur-22.0.0 %build %py3_build %install %py3_install install -d -m755 %{buildroot}/%{_pkgdocdir} if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi pushd %{buildroot} if [ -d usr/lib ]; then find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/lib64 ]; then find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/bin ]; then find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/sbin ]; then find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst fi touch doclist.lst if [ -d usr/share/man ]; then find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst fi popd mv %{buildroot}/filelist.lst . mv %{buildroot}/doclist.lst . %files -n python3-nextstrain-augur -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Mon May 15 2023 Python_Bot - 22.0.0-1 - Package Spec generated