Installing the container-based Nextstrain CLI

The Nextstrain command-line tool (CLI) aims to provide access to Nextstrain components in a local environment with minimal fuss. It uses docker containers to bundle up the installation of all the components behind Nextstrain, so that you have a clean interface and fewer installation issues!

Once you’ve installed the Nextstrain CLI, you can run the quickstart guide or any of the tutorials available here.

Before digging in, it’s worth reading the difference between a local and container installation, both of which will install the components behind Nextstrain and allow you to run and visualize analyses on your computer.

Table of Contents:


Python 3.5 or newer

This tool is written in Python 3 and requires at least Python 3.5. There are many ways to install Python 3 on Windows, macOS, or Linux, including the official packages, Homebrew for macOS, and the Anaconda Distribution. Details are beyond the scope of this guide, but make sure you install Python 3.5 or higher. You may already have Python 3 installed, especially if you’re on Linux. Check by running python --version or python3 --version.


Git is a version control system used by all of the Nextstrain ecosystem. It is free to download and install.

Install the Nextstrain CLI

With Python 3 installed, you can use pip to install the Nextstrain-CLI package:

$ python3 -m pip install nextstrain-cli
Collecting nextstrain-cli
[…a lot of output…]
Successfully installed nextstrain-cli-1.6.1

After installation, make sure the nextstrain command works by running nextstrain version:

$ nextstrain version
nextstrain.cli 1.6.1

The version you get will probably be different than the one shown in the example above.

Install Docker

This tool also currently requires Docker, which is freely available. On Windows or a Mac you should download and install Docker Desktop (also known as “Docker for Mac” and “Docker for Windows”). On Linux, your package manager should include a Docker package.

After installing Docker, run nextstrain check-setup to ensure it works:

$ nextstrain check-setup
nextstrain-cli is up to date!

Testing your setup…

✔ docker is installed
✔ docker run works

All good!

If the final message doesn’t indicate success (as with “All good!” in the example above), something may be wrong with your Docker installation. Please get in touch with us if this is the case!


This package provides a nextstrain program which provides access to a few commands. If you’ve installed this package (nextstrain-cli), you can just run nextstrain. Otherwise, you can run ./bin/nextstrain from a copy of the source code.

usage: nextstrain [-h] {build,view,deploy,shell,update,check-setup,version} ...

Nextstrain command-line tool

optional arguments:
  -h, --help            show this help message and exit

    build               Run pathogen build
    view                View pathogen build
    deploy              Deploy pathogen build
    shell               Start a new shell in the build environment
    update              Updates your local image copy
    check-setup         Tests your local setup
    version             Show version information

For more information on a specific command, you can run it with the --help option, for example, nextstrain build --help.


Development of nextstrain-cli happens at Please see the README there for further information.

All source code is freely available under the terms of the GNU Affero General Public License. Screenshots may be used under a CC-BY-4.0 license and attribution to must be provided.

This work is made possible by the open sharing of genetic data by research groups from all over the world. We gratefully acknowledge their contributions. Special thanks to Kristian Andersen, David Blazes, Peter Bogner, Matt Cotten, Ana Crisan, Gytis Dudas, Vivien Dugan, Karl Erlandson, Nuno Faria, Jennifer Gardy, Becky Kondor, Dylan George, Ian Goodfellow, Betz Halloran, Christian Happi, Jeff Joy, Paul Kellam, Philippe Lemey, Nick Loman, Sebastian Maurer-Stroh, Oliver Pybus, Andrew Rambaut, Colin Russell, Pardis Sabeti, Katherine Siddle, Kristof Theys, Dave Wentworth, Shirlee Wohl and Nathan Yozwiak for comments, suggestions and data sharing.


© 2015-2020 Trevor Bedford and Richard Neher