Local Installation

The following instructions describe how to install augur (bioinformatics tooling) and auspice (our visualization app) together, in the same Conda environment, on macOS or an Ubuntu-style Linux distribution.

Before digging in, it’s worth reading about the different installation methods which will install the components behind Nextstrain and allow you to run and visualize analyses on your computer.

If you would prefer to install each component individually, please see the respective installation guides using the links in the sidebar. If you are using Windows, we have instructions for installing a Linux subsystem to get Nextstrain running. If you have any issues with installing Augur/Auspice using any of these methods, please email us or submit a GitHub issue to Augur or Auspice.

Install Augur & Auspice with Conda

Download and install the latest version of Miniconda with Python 3 which will make the conda command available to you. If you already have Miniconda installed with Python 2, download the latest Python 3 version and follow conda’s installation instructions. If you already have an older Miniconda version installed with Python 3, you may need to update your installation prior to installing Nextstrain’s tools with:

conda activate base
conda update conda

We’re going to create a new environment called “nextstrain”, which automatically installs Augur and dependencies. We’ll then install Auspice into this environment as well, and optionally set up the Nextstrain command.

curl http://data.nextstrain.org/nextstrain.yml --compressed -o nextstrain.yml
conda env create -f nextstrain.yml
conda activate nextstrain
npm install --global auspice

# Optionally, if you want to use the nextstrain command
nextstrain check-setup --set-default

and we’re all done 🙌. The beauty of this is that whenever you want to use augur or auspice you can jump into the nextstrain conda environment and you’re good to go!

conda activate nextstrain

# Test things are installed / run analyses
augur -h
auspice -h
nextstrain -h

# When you're done, leave the environment
conda deactivate

Update an existing installation

The following commands presume you have installed the software via the method described above.

First, update the base conda environment.

conda activate base
conda update conda

Then, update each individual program, as necessary.

conda activate nextstrain

# Update Nextstrain dependencies (mafft, etc.).
conda update --all

# Update Augur.
python3 -m pip install --upgrade nextstrain-augur

# Update Auspice.
npm update --global auspice

# Update the Nextstrain CLI and pull the latest Docker image.
python3 -m pip install --upgrade nextstrain-cli
nextstrain update