This page describes how to upgrade the Nextstrain CLI–the nextstrain command–itself, without also upgrading the entire Nextstrain runtime.

The first step is to figure out what kind of Nextstrain CLI installation you have.

If you run conda activate nextstrain before running nextstrain commands, then you’re using a Conda-based installation like we describe in the Nextstrain installation steps. In this case, run the following to upgrade:

conda activate nextstrain
mamba update -c conda-forge -c bioconda nextstrain-cli

Otherwise, you’re using another installation method and running:

$ nextstrain check-setup
A new version of nextstrain-cli, X.Y.Z, is available!  You're running A.B.C.

Upgrade by running:


Testing your setup…

will suggest a command to run to upgrade nextstrain. Run the suggested command to perform the upgrade.

Either way, you can check the new version that was installed by running:

$ nextstrain version
nextstrain.cli 3.2.1