Ambient runtime

Run commands in the ambient environment, outside of any container image or managed environment.

The “ambient” runtime allows you to use the Nextstrain CLI with your own ambient setup, for when you cannot or do not want to have Nextstrain CLI manage its own runtime.

New in version 1.5.0.

Changed in version 5.0.0: Renamed from “native” to “ambient”.


You will need to make sure all of the Nextstrain software dependencies are available locally or “ambiently” on your computer.

A common way to do this is by manually using Conda to manage your own environment that includes the required software, however you’re responsible for making sure the correct software is installed and kept up-to-date. Our general Nextstrain installation page describes more comprehensively how to do this.

It is also possible to install the required Nextstrain software Augur and Auspice and their dependencies manually, although this is not recommended.

Once you’ve installed dependencies, proceed with nextstrain setup ambient.