Nextstrain CLI
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 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 and Auspice
computing platforms, such as
Docker runtime,
Conda runtime,
Singularity runtime, and
AWS Batch runtime.
Note
If you’re unfamiliar with Nextstrain builds, you may want to follow our Running a phylogenetic workflow tutorial first and then come back here.
Table of Contents
Commands
- nextstrain build
- nextstrain view
- nextstrain deploy
- nextstrain remote
- nextstrain remote list
- nextstrain remote download
- nextstrain remote upload
- nextstrain remote delete
- nextstrain shell
- nextstrain update
- nextstrain setup
- nextstrain check-setup
- nextstrain login
- nextstrain logout
- nextstrain whoami
- nextstrain authorization
- nextstrain version
Remotes
Configuration
Development
Big Picture
The Nextstrain CLI glues together many different components. Below is a brief overview of the big picture:
