Installing Nextstrain

Hint

Before installing, we recommend you read about the parts of Nextstrain.

The following instructions describe how to install the full suite of Nextstrain’s software tools, including:

  • Nextstrain CLI, for access to other tools and management of workflows

  • Augur, for bioinformatic analysis of pathogen genomes

  • Auspice, for interactive visualization of pathogen evolution

When completed, you’ll be ready to run Nextstrain workflows.

Installation steps

Steps vary by runtime option (Docker, Conda, ambient) and host interface (macOS, Windows (WSL), Windows (PowerShell), Linux). For help choosing, refer to our Frequently Asked Questions (FAQ), such as:

Install Nextstrain CLI

In a Terminal, run:

curl -fsSL --proto '=https' https://nextstrain.org/cli/installer/mac | bash

You can launch a Terminal by clicking the Launchpad icon in the Dock, typing terminal in the search field, and clicking Terminal.

Note

On newer Macs with an Apple silicon chip (e.g. M1), Rosetta 2 is required for both Nextstrain CLI itself and our runtimes. Most of the time, Rosetta 2 will already be enabled. If not, the installer will ask you to first enable Rosetta 2 and then retry the installation.

Make sure to follow the installer’s final instructions to setup your shell config.

Set up a Nextstrain runtime

  1. Install Docker on your computer.

  2. Set up the runtime:

    nextstrain setup --set-default docker
    

The final output from the last command should look like this, where <runtime> is the runtime option (e.g. Docker, Conda, or ambient) chosen in the first step:

Setting default environment to <runtime>.

All good!  Set up of <runtime> complete.

Optionally, configure AWS Batch if you’d like to run nextstrain build on AWS.

Try running Augur and Auspice

  1. Enter an interactive Nextstrain shell in the current directory (.).

    nextstrain shell .
    
  2. Run Augur.

    augur --help
    
  3. Run Auspice.

    auspice --help
    
  4. Exit the Nextstrain shell.

    exit
    

Next steps

With Nextstrain installed, try Running a pathogen workflow next.

Alternate installation methods

If you want to contribute to the development of Nextstrain or if you prefer to manage your own custom environment (e.g., a Conda environment, Docker image, environment modules on a cluster, etc.), see the individual installation documentation for Nextstrain CLI, Augur, and Auspice.

Managing an existing installation

See Managing a Nextstrain Installation for steps to update, troubleshoot, or uninstall Nextstrain tools.