The Nextstrain command-line interface (CLI)—a program called nextstrain—which aims to provide a consistent way to run and visualize pathogen builds and access Nextstrain components like Augur and Auspice across computing environments such as Docker, Conda, and AWS Batch.


Python 3.6 or newer

This program is written in Python 3 and requires at least Python 3.6. 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 3.6 or higher. You may already have Python 3 installed, especially if you’re on Linux. Check by running python --version or python3 --version.


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-1.16.5

This package also works great with Pipx, a nice alternative to Pip for command-line apps like this one:

$ pipx install nextstrain-cli
Installing to directory '/home/tom/.local/pipx/venvs/nextstrain-cli'
  installed package nextstrain-cli 1.16.5, Python 3.6.9
  These apps are now globally available
    - nextstrain
done! ✨ 🌟 ✨

Either way you choose, make sure the nextstrain command is available after installation by running nextstrain version:

$ nextstrain version
nextstrain.cli 1.16.5

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

Computing environment

The Nextstrain CLI provides a consistent interface for running and visualizing Nextstrain pathogen builds across several different computing environments, such as Docker, Conda, and AWS Batch. Each computing environment provides specific versions of Nextstrain’s software components and is responsible for running Nextstrain’s programs like Augur and Auspice. For this reason, the different computing environments are called “runners” by the CLI.

At least one of these computing environments, or runners, must be setup in order for many of nextstrain’s subcommands to work, such as nextstrain build and nextstrain view.

The default runner is Docker, using the nextstrain/base container image. Containers provide a tremendous amount of benefit for scientific workflows by isolating dependencies and increasing reproducibility. However, they’re not always appropriate, so a “native” runner is also supported. The installation and setup of supported runners is described below.


Docker is a very popular container system freely-available for all platforms. When you use Docker with the Nextstrain CLI, you don’t need to install any other Nextstrain software dependencies as validated versions are already bundled into a container image by the Nextstrain team.

On macOS, download and install Docker Desktop, also known previously as “Docker for Mac”.

On Linux, install Docker with the standard package manager. For example, on Ubuntu, you can install Docker with sudo apt install

On Windows, there are still significant obstacles to running with Docker, as documented in our issue tracking the problems. However, if you have access to WSL2, you should be able to use Docker inside it by following the Linux install instructions. Alternatively, you can use the native or AWS Batch runners.

Once you’ve installed Docker, proceed with checking your setup.


The “native” runner allows you to use the Nextstrain CLI without installing Docker, for cases when you cannot or do not want to use containers.

However, you will need to make sure all of the Nextstrain software dependencies are available locally or “natively” on your computer. The easiest and most common way to do this is by using Conda to install our Conda environment, as documented here. It is also possible to install the required Nextstrain software Augur and Auspice and their dependencies manually, although this is not recommended.

Once you’ve installed dependencies, proceed with checking your setup.

AWS Batch

AWS Batch is an advanced computing environment which allows you to launch and monitor Nextstrain builds in the cloud from the comfort of your own computer. The same image used by the local Docker runner is used by AWS Batch, making your builds more reproducible, and builds have access to computers with very large CPU and memory allocations if necessary.

The initial setup is quite a bit more involved, but detailed instructions are available.

Once you’ve setup AWS, proceed with checking your setup.

Checking your setup

After installation and setup, run nextstrain check-setup --set-default to ensure everything works and automatically pick an appropriate default runner based on what’s available. You should see output similar to the following:

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

Testing your setup…

# docker is supported
✔ yes: docker is installed
✔ yes: docker run works
✔ yes: containers have access to >2 GiB of memory
✔ yes: image is new enough for this CLI version

# native is not supported
✔ yes: snakemake is installed
✘ no: augur is installed
✘ no: auspice is installed

# aws-batch is not supported
✘ no: job description "nextstrain-job" exists
✘ no: job queue "nextstrain-job-queue" exists
✘ no: S3 bucket "nextstrain-jobs" exists

All good!  Supported Nextstrain environments: docker

Setting default environment to docker.

If the output doesn’t say “All good!” and list at least one supported Nextstrain computing environment (typically Docker or native), then something may be wrong with your installation.

The default is written to the ~/.nextstrain/config file. If multiple environments are supported, you can override the default for specific runs using command-line options such as --docker, --native, and --aws-batch, e.g. nextstrain build --native ….