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 respecive 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 which will make the
conda command available to you.
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
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
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
conda activate nextstrain pip install --upgrade nextstrain-augur nextstrain-cli npm update --global auspice