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.