nextstrain setup

Sets up a Nextstrain runtime for use with nextstrain build, nextstrain view, etc.

Only the Conda runtime currently supports automated set up, but this command may still be used with other runtimes to check an existing (manual) setup and set the runtime as the default on success.

Exits with an error code if automated set up fails or if setup checks fail.

usage: nextstrain setup [-h] [--dry-run] [--force] [--set-default] <runtime>

Positional Arguments


The Nextstrain runtime to set up. One of {docker, conda, singularity, ambient, aws-batch}.

Named Arguments


Don’t actually set up anything, just show what would happen.

Default: False


Ignore existing setup, if any, and always start fresh.

Default: False


Use the runtime as the default if set up is successful.

Default: False