Using pip from PyPi¶
python3 -m pip install nextstrain-augur
Augur uses some common external bioinformatics programs which you’ll need to install to have a fully functioning toolkit:
augur alignrequires mafft
augur treerequires at least one of:
Bacterial data (or any VCF usage) requires vcftools
On macOS, you can install 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.
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
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 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 “editable” 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 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.