Hint
This is reference documentation for the Nextstrain CLI (command-line interface). If you're just getting started with Nextstrain, please see our general documentation <docs:index> instead.
The Nextstrain CLI is a program called nextstrain. It aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur <augur:index> and Auspice <auspice:index> across computing environments such as Docker, Conda, and AWS Batch.
Note
If you're unfamiliar with Nextstrain builds, you may want to follow our docs:tutorials/running-a-workflow tutorial first and then come back here.
Introduction <self> installation upgrading AWS Batch <aws-batch>
commands/build commands/view commands/deploy commands/remote/index commands/remote/list commands/remote/download commands/remote/upload commands/remote/delete commands/shell commands/update commands/check-setup commands/login commands/logout commands/whoami commands/version
nextstrain.org <remotes/nextstrain.org> Amazon S3 <remotes/s3>
The Nextstrain CLI glues together many different components. Below is a brief overview of the big picture:
genindexsearch