nextstrain.org remote

Added in version 3.1.0.

The nextstrain remote family of commands can list, download, upload, and delete Nextstrain datasets and narratives hosted on nextstrain.org. This functionality is primarily intended for users to manage the contents of their Nextstrain Groups, but any public dataset or narrative may be downloaded.

Remote paths

Nextstrain.org datasets and narratives are recognized by the same URLs used to view them on the web, e.g. https://nextstrain.org/ncov/open/global.

As a convenience, the scheme (https://) may be omitted, e.g. nextstrain.org/ncov/open/global.

As a further convenience for Nextstrain Groups URLs, the domain (nextstrain.org) may also be omitted, e.g. groups/blab/sars-like-cov works as well as https://nextstrain.org/groups/blab/sars-like-cov.

Authentication

Read-only actions may be performed against public paths without authentication. To manage a private Nextstrain Group or upload/delete a public path, first login with nextstrain.org credentials using the nextstrain login command.

Environment variables

Warning

For development only. You don’t need to set these during normal operation.

NEXTSTRAIN_DOT_ORG

Base URL to use instead of https://nextstrain.org when accessing remote resources, e.g.:

NEXTSTRAIN_DOT_ORG=http://localhost:5000 nextstrain remote ls nextstrain.org

will interact with http://localhost:5000 instead of nextstrain.org.

NEXTSTRAIN_DISABLE_NARRATIVE_IMAGE_EMBEDDING: Set to any non-empty value to disable the automatic embedding of local images into narratives during upload. The narrative’s Markdown contents will be uploaded as-is, but any local images referenced by it will almost certainly be broken.