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, Singularity, and AWS Batch.

Run nextstrain <command> --help for usage information about each command. See <Nextstrain CLI> for more documentation.

options

-h, --help

show this help message and exit

commands

build

Run pathogen build. See nextstrain build.

view

View pathogen builds and narratives. See nextstrain view.

deploy

Deploy pathogen build. See nextstrain deploy.

remote

Upload, download, and manage remote datasets and narratives.. See nextstrain remote.

shell

Start a new shell in a runtime. See nextstrain shell.

update

Update a runtime. See nextstrain update.

setup

Set up a runtime. See nextstrain setup.

check-setup

Check runtime setups. See nextstrain check-setup.

login

Log into Nextstrain.org (and other remotes). See nextstrain login.

logout

Log out of Nextstrain.org (and other remotes). See nextstrain logout.

whoami

Show information about the logged-in user. See nextstrain whoami.

version

Show version information. See nextstrain version.

init-shell

Print shell init script. See nextstrain init-shell.

authorization

Print an HTTP Authorization header. See nextstrain authorization.

debugger

Start a debugger. See nextstrain debugger.