Help! I'm using Windows

Nextstrain documentation assumes users are running a Unix-based system like Mac OS X or Linux. It is in theory possible to install and run Nextstrain components in Windows natively, but it will be less straightforward, and won’t be covered here.

However, a new feature in Windows 10 means you can easily run a ‘subsystem’ of Linux on your Windows machine, ensuring you’ll be able to use exactly the same commands as given in the documentation.

After installing, you may want to Google for some information (or a tutorial) on basic Linux commands. This guide will assume you’re relatively new to Linux/Ubuntu; if you’re a more advanced user you may want to modify the instructions to suit your preferences.

Enable and Install Ubuntu via Microsoft Store

The Windows Subsystem for Linux is developed and supported by Microsoft, so it will not cause any problems for your computer. It is not a ‘dual-boot’ system, where you must restart to switch between Windows and Ubuntu; you’ll be able to run Ubuntu in a window within Windows. Though multiple Linux distributions are now available, we recommend installing Ubuntu, as it has lots of support available online for Windows 10 installations.

Follow these instructions to install Windows Subsystem for Linux, and select ‘Ubuntu’ from the Store. Be sure to follow the instructions for ‘initialization of your distro’, and update/upgrade Ubuntu using

sudo apt update && sudo apt upgrade

Take note of your password; you’ll need this whenever you run sudo commands (like running ‘as administrator’ in Windows).

You can start Ubuntu on Windows by going to the Start Menu and selecting ‘Ubuntu’. The default working directory (your location on starting Ubuntu) is buried in an odd place within the Windows filesystem. You probably don’t want to put files here, as they’ll be hard to find from Windows applications.

Instead, we’ll make a ‘symbolic link’ or ‘symlink’ (like a ‘shortcut’ in Windows) so you can easily jump to the directory where your files are stored. Here, we’ll make a symlink to C:\Users\<user>\Documents (replace <user> with your username), but you could point it to wherever would be useful for you.

The first part (../../mnt/c/Users/<user>/Documents) is where you’d like the link to go (mnt/c/ is how to access the C: drive from here in Ubuntu), and documents is the name of the symlink.

ln -s ../../mnt/c/Users/<user>/Documents documents

To use the symlink, just type cd documents - you’ll go directly to the usual ‘Documents’ folder in Windows. You might want to get into the habit of using cd documents immediately whenever you start Ubuntu, so that files you download and run are always in the same place.

Install Miniconda

Miniconda allows you to create ‘environments’ within Ubuntu and more easily install some packages. We’ll do this to make the installation of some Nextstrain components easier.

Download the latest Python 3.6 Linux version of Miniconda. You may want to move the download to inside the folder your symlink leads to, to make it easier to navigate to the file location within Ubuntu.

Once inside the folder with the file you downloaded, type bash followed by the name of the file you downloaded. For example:


Follow the prompts and accept the defaults if you are unsure. You’ll need to close and re-open your Ubuntu window to finish the installation.

After re-opening Ubuntu, you can type conda list to ensure it’s installed correctly.

When you install augur, you can now follow the instructions to install augur with Conda. Don’t do this just yet - finish installing things below!

You’ll always need to use conda activate nextstrain before running augur.

Installing Necessary Programs

It’s important to remember that to install things in Ubuntu you will not be able to follow the usual Windows installation instructions. You also generally can’t use things you’ve already installed in Windows when working in Ubuntu - you’ll need to install them again in Ubuntu.

But, installing the things you’ll need to run Nextstrain is very easy.

(If you already have any of the below installed, it will tell you, and nothing will be changed.)

Install git & gcc

Git will allow you to ‘clone’ or copy files from GitHub, which is where all the Nextstrain code and public data lives. gcc is a compiler used by some packages.

Install both with:

sudo apt-get install git
sudo apt-get install gcc

Install Node.js & npm

The easiest way to install Node.js and npm is via nvm. You can follow Step 0 from these instructions, repeated here:

Download and install nvm:

curl -o- | bash

After it finishes, close and re-open Ubuntu to complete the install, then check it by typing nvm --version.

Now finish setting it up by running:

nvm install node
nvm use node
nvm install --lts
nvm use --lts

Install Nextstrain

You’re now ready to install Nextstrain programs! You should already now have Python 3 and git, so jump to installing augur with Conda.

When you install auspice, you already have Node.js.

Important Note:

Never modify your Ubuntu system files (like .bashrc) in Windows! Use an editor within Ubuntu, like vi or vim.

All source code is freely available under the terms of the GNU Affero General Public License. Screenshots etc may be used as long as a link to is 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, Allison Black, David Blazes, Peter Bogner, Matt Cotten, Ana Crisan, Gytis Dudas, Vivien Dugan, Karl Erlandson, Nuno Faria, Jennifer Gardy, Becky Garten, Dylan George, Ian Goodfellow, Nathan Grubaugh, Betz Halloran, Christian Happi, Jeff Joy, Paul Kellam, Philippe Lemey, Nick Loman, Sebastian Maurer-Stroh, Louise Moncla, 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.


© 2015-2019 Trevor Bedford and Richard Neher