python -m pip install nextstrain-augur
You can also install from a git clone or other copy of the source code by running:
python -m 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 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 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
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.