This is an Augur-specific installation guide. If you wish to use Nextstrain as a whole, please refer to the Nextstrain installation guide.
Augur uses some external bioinformatics programs:
augur alignrequires mafft
augur treerequires at least one of:
Bacterial data (or any VCF usage) requires vcftools
If you use Conda or Mamba, you can install them in an active environment:
conda install -c conda-forge -c bioconda mafft raxml fasttree iqtree vcftools --yes
On macOS using Homebrew:
brew tap brewsci/bio brew install mafft iqtree raxml fasttree vcftools
sudo apt install mafft iqtree raxml fasttree vcftools
Other Linux distributions will likely have the same packages available, although the names may differ slightly.
Install Augur as a user
This assumes you have Conda installed and an environment active. If not, refer to instructions for ambient runtime setup on the Nextstrain installation guide.
conda install -c conda-forge -c bioconda augur
If you encounter environment solving errors or want a faster installation process, use mamba as a drop-in replacement for conda:
mamba install -c conda-forge -c bioconda augur
Using pip from PyPi
Augur is written in Python 3 and requires at least Python 3.7. It’s published on PyPi as nextstrain-augur, so you can install it with
pip like so:
python3 -m pip install nextstrain-augur
git clone https://github.com/nextstrain/augur.git python3 -m pip install .
This installs Augur along with external Python dependencies.
Install Augur as a developer
python3 -m pip install -e '.[dev]'
This installs dependencies necessary for local development.
Testing if it worked
If installation worked, you should be able to run
augur --help and see augur’s primary help output.