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 3.4. It's published on PyPi as nextstrain-augur, so you can install it with pip like so:

pip install nextstrain-augur

You can also install from a git clone or other copy of the source code by running:

pip install .

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

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

conda activate augur

Testing if it worked

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