Installation
Note
This is an Augur-specific installation guide. If you wish to use Nextstrain as a whole, please refer to the Nextstrain installation guide.
Installing dependencies
Augur uses some external bioinformatics programs:
augur align
requires mafftaugur tree
requires 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
On Debian/Ubuntu:
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
Using Mamba
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
From source
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.