Pipeline components for real-time phylodynamic analysis
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Installation


Using pip from PyPi

Augur is written in Python 3 and requires at least Python 3.6. It's published on PyPi as nextstrain-augur, so you can install it with pip like so:

pip install nextstrain-augur

If your system has both Python 2 and Python 3 installed side-by-side, you may need to use python3 instead of just python (which often defaults to Python 2 when both Python versions are installed).

Augur uses some common external bioinformatics programs which you'll need to install to have a fully functioning toolkit:

  • augur align requires mafft

  • augur tree requires at least one of:

  • Bacterial data (or any VCF usage) requires vcftools

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

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.

Using Conda

Alternatively, augur itself and all of its dependencies can be installed into a Conda 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 <your-env-name>

When that finishes, the enviroment needs to be activated whenever you want to use augur:

conda activate augur

Install from source

git clone https://github.com/nextstrain/augur.git
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:

pip install .[full]

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

pip install -e .[dev]

See above for how to install the external bioinformatics programs which you'll need to have a fully functioning toolkit.

Testing if it worked

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