nextstrain update

usage: nextstrain update [<pathogen-name>[@<version>] | <runtime-name> […]]
       nextstrain update
       nextstrain update --help

Updates Nextstrain pathogens and runtimes to the latest available versions, if any.

When this command is run without arguments, the default version for each set up pathogen (none) and the default runtime (docker) are updated. Provide one or more pathogens and/or runtimes as arguments to update a select list instead.

Three runtimes currently support updates: Docker, Conda, and Singularity. Updates may take several minutes as new software versions are downloaded.

This command also checks for newer versions of the Nextstrain CLI (the nextstrain program) itself and will suggest upgrade instructions if an upgrade is available.

positional arguments

<pathogen>|<runtime>

The Nextstrain pathogens and/or runtimes to update.

A pathogen is the name (and optionally, version) of a previously set up pathogen. See nextstrain setup. If no version is specified, then the default version will be updated to the latest available version.

A runtime is one of {docker, conda, singularity, ambient, aws-batch}.

options

-h, --help: show this help message and exit