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

<runtime>

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

Named Arguments

--dry-run

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

Default: False

--force

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

Default: False

--set-default

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

Default: False