This page describes how to upgrade the Nextstrain CLI–the
command–itself, without also upgrading the entire Nextstrain
The first step is to figure out what kind of Nextstrain CLI installation you have.
If you run
conda activate nextstrain before running
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: [UPGRADE COMMAND] 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