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.. program:: nextstrain
usage: nextstrain [-h] {build,view,deploy,remote,shell,update,setup,check-setup,login,logout,whoami,version,init-shell,authorization,debugger} ...
Nextstrain command-line interface (CLI)
The nextstrain
program and its subcommands aim to provide a consistent way to
run and visualize pathogen builds and access Nextstrain components like Augur
and Auspice across computing platforms such as Docker, Conda, and AWS Batch.
Run nextstrain <command> --help
for usage information about each command.
See <:doc:`/index`> for more documentation.
.. option:: -h, --help show this help message and exit
.. option:: build Run pathogen build. See :doc:`/commands/build`.
.. option:: view View pathogen builds and narratives. See :doc:`/commands/view`.
.. option:: deploy Deploy pathogen build. See :doc:`/commands/deploy`.
.. option:: remote Upload, download, and manage remote datasets and narratives.. See :doc:`/commands/remote/index`.
.. option:: shell Start a new shell in a runtime. See :doc:`/commands/shell`.
.. option:: update Update a runtime. See :doc:`/commands/update`.
.. option:: setup Set up a runtime. See :doc:`/commands/setup`.
.. option:: check-setup Check runtime setups. See :doc:`/commands/check-setup`.
.. option:: login Log into Nextstrain.org (and other remotes). See :doc:`/commands/login`.
.. option:: logout Log out of Nextstrain.org (and other remotes). See :doc:`/commands/logout`.
.. option:: whoami Show information about the logged-in user. See :doc:`/commands/whoami`.
.. option:: version Show version information. See :doc:`/commands/version`.
.. option:: init-shell Print shell init script. See :doc:`/commands/init-shell`.
.. option:: authorization Print an HTTP Authorization header. See :doc:`/commands/authorization`.
.. option:: debugger Start a debugger. See :doc:`/commands/debugger`.