nextstrain setup

usage: nextstrain setup [--dry-run] [--force] [--set-default] <pathogen-name>[@<version>[=<url>]]
       nextstrain setup [--dry-run] [--force] [--set-default] <runtime-name>
       nextstrain setup --help

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

For pathogens, set up involves downloading a specific version of the pathogen’s Nextstrain workflows. By convention, this download is from Nextstrain’s repositories. More than one version of the same pathogen may be set up and used independently. This can be useful for comparing analyses across workflow versions. A default version can be set.

For runtimes, only the Conda runtime currently supports fully-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.

positional arguments

<pathogen>|<runtime>

The Nextstrain pathogen or runtime to set up.

A pathogen is usually the plain name of a Nextstrain-maintained pathogen (e.g. measles), optionally with an @<version> specifier (e.g. measles@v42). If <version> is specified in this case, it must be a tag name (i.e. a release name), development branch name, or a development commit id.

A pathogen may also be fully-specified as <name>@<version>=<url> where <name> and <version> in this case are (mostly) arbitrary and <url> points to a ZIP file containing the pathogen repository contents (e.g. https://github.com/nextstrain/measles/zipball/83b446d67fc03de2ce1c72bb1345b4c4eace7231).

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

options

-h, --help

show this help message and exit

--dry-run

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

--force

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

--set-default

Use this pathogen version or runtime as the default if set up is successful.