Installationļƒ


Using condaļƒ

Install Miniconda with Python 3. If you already have Miniconda installed with Python 2, download the latest Python 3 version and follow condaā€™s installation instructions. If you already have an older Miniconda version installed with Python 3, you may need to update your installation prior to installing Nextstrainā€™s tools with:

conda activate base
conda update conda

Create a conda environment to install augur into and activate that environment.

conda create -n nextstrain
conda activate nextstrain

Install augur and its dependencies into your environment.

conda install -c conda-forge -c bioconda augur

For a much faster installation process, use mamba as a drop-in replacement for conda.

conda install -c conda-forge mamba
mamba install -c conda-forge -c bioconda augur

Using pip from PyPiļƒ

Augur is written in Python 3 and requires at least Python 3.7. Itā€™s published on PyPi as nextstrain-augur, so you can install it with pip like so:

python3 -m pip install nextstrain-augur

Augur uses some common external bioinformatics programs which youā€™ll need to install to have a fully functioning toolkit:

  • Nextstrain workflows and some tutorials require Snakemake

  • augur align requires mafft

  • augur tree requires at least one of:

  • Bacterial data (or any VCF usage) requires vcftools

On macOS, you can install most of these external programs using Homebrew with:

brew tap brewsci/bio
brew install mafft iqtree raxml fasttree vcftools

On Debian/Ubuntu, you can install them via:

sudo apt install mafft iqtree raxml fasttree vcftools

Other Linux distributions will likely have the same packages available, although the names may differ slightly. Follow Snakemakeā€™s installation instructions for your operating system.

Install from sourceļƒ

git clone https://github.com/nextstrain/augur.git
python3 -m pip install .

This install depends on a fairly minimal set of external Python libraries. There are some functions in augur that require a larger set of dependencies. These can be installed via:

python3 -m pip install '.[full]'

If you wish to also install the development dependencies, and install augur in an ā€œeditableā€ mode whereby changes to the source code are reflected in your version of augur then run:

python3 -m pip install -e '.[dev]'

See above for how to install the external bioinformatics programs which youā€™ll need to have a fully functioning toolkit.

Testing if it workedļƒ

If installation worked, you should be able to run augur --help and see augurā€™s primary help output.