diff --git a/DEV_DOCS.md b/DEV_DOCS.md index 36e2eba5f..aae603cd7 100644 --- a/DEV_DOCS.md +++ b/DEV_DOCS.md @@ -6,7 +6,8 @@ Thank you for helping us to improve Nextstrain! This document describes: - Contributing code - Running local code changes - Testing - - Creating a release + - Releasing + - Maintaining Bioconda package - Continuous integration - Contributing documentation - Formats (Markdown and reStructuredText) @@ -170,6 +171,16 @@ If any tests fail, run the `./devel/rewind-release` script to undo the release, [a PyPi account]: https://pypi.org/account/register/ [twine]: https://pypi.org/project/twine +### Maintaining Bioconda package + +Bioconda hosts [augur’s conda package](http://bioconda.github.io/recipes/augur/README.html) and defines augur’s dependencies in [a conda recipe YAML file](https://github.com/bioconda/bioconda-recipes/blob/master/recipes/augur/meta.yaml). +New releases on GitHub automatically trigger a new Bioconda release. + +To modify augur’s dependencies or other aspects of its conda environment, [follow Bioconda’s contributing guide](https://bioconda.github.io/contributor/index.html). +You will need to update the existing recipe YAML locally and create a pull request on GitHub for testing and review. +Add your GitHub username to the `recipe_maintainers` list, if this is your first time modifying the augur recipe. +After a successful pull request review, Bioconda will automatically update the augur package that users download. + ### Travis CI Branches and PRs are tested by Travis CI jobs configured in `.travis.yml`. diff --git a/README.md b/README.md index 4d61e6cf9..db07ecc3e 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@ [![Build Status](https://travis-ci.com/nextstrain/augur.svg?branch=master)](https://travis-ci.com/nextstrain/augur) [![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://nextstrain-augur.readthedocs.io/en/stable/?badge=latest) [![License: AGPL v3](https://img.shields.io/badge/License-AGPL%20v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0) diff --git a/docs/installation/installation.md b/docs/installation/installation.md index 806b09e0a..c963ab713 100644 --- a/docs/installation/installation.md +++ b/docs/installation/installation.md @@ -1,12 +1,35 @@ # Installation +* [Using conda](#using-conda) * [Using pip from PyPi](#using-pip-from-pypi) -* [Using Conda](#using-conda) * [Install from source](#install-from-source) * [Testing if it worked](#testing-if-it-worked) --- +## Using conda + +Install [Miniconda](https://docs.conda.io/en/latest/miniconda.html). +Create a conda environment to install augur into and activate that environment. + +```bash +conda create -n nextstrain +conda activate nextstrain +``` + +Install augur and its dependencies into your environment. + +```bash +conda install -c conda-forge -c bioconda augur +``` + +For a much faster installation process, use [mamba](https://github.com/TheSnakePit/mamba) as a drop-in replacement for conda. + +```bash +conda install -c conda-forge mamba +mamba install -c conda-forge -c bioconda augur +``` + ## Using pip from PyPi Augur is written in Python 3 and requires at least Python 3.6. @@ -41,18 +64,6 @@ On Debian/Ubuntu, you can install them via: Other Linux distributions will likely have the same packages available, although the names may differ slightly. Follow [Snakemake's installation instructions](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html) for your operating system. -## Using Conda - -Alternatively, augur itself and all of its dependencies can be installed into a [Conda](https://conda.io/miniconda.html) environment: - - conda env create -f environment.yml - -> _By default this environment is named "augur" but you can change that by providing a name to the above command with `-n `_ - -When that finishes, the enviroment needs to be activated whenever you want to use augur: - - conda activate augur - ## Install from source ```bash