How do I set up Windows 10 to run SPAdes and Flye assemblers?

The assemblers SPAdes (Geneious 10.1+) and Flye (Geneious Prime 2020.1+) can normally only run on a 64-bit Linux system or Mac OS.  However within Geneious it is possible to run these on a 64-bit Windows 10 system if you install Windows Subsystem for Linux, following the setup instructions below.  You must be using Windows 10 Pro with all recent updates installed.

Instructions for installing Windows Subsystem for Linux on Windows 10. 

  1. Run PowerShell as Admin – from the Start menu, right-click on Windows PowerShell > Windows PowerShell, then select 'Run as Administrator'.
  2. At the terminal prompt, type 'Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux'.
  3. Wait for Windows Subsystem for Linux installation to complete, then restart your computer if Windows prompts you to do so.
  4. Open the Microsoft Store app, and search for and install 'Ubuntu 16.04 LTS'.
  5. Wait until the installation window disappears (this may take a few minutes). Note: if this step fails, please make sure you have installed all recent updates for Windows 10.
  6. Open Ubuntu 16.04 LTS from the Start menu. This may take some time as Ubuntu is set up for the first time. You’ll be prompted to create a username and password (these don't need to be the same as your Windows username/password). 

Note: If you are using Geneious 10.2.6 or earlier, you need to run the following additional command after creating your Ubuntu username and password:  

sudo bash -c "ln -s /usr/bin/python3 /usr/local/bin/python"

You can now close Ubuntu, and you should be able to run SPAdes or Flye on your Windows 10 machine (until you have run them for the first time the message about setting this up will still show, but it should now run if you click 'OK').  Note that Flye is an external plugin and must be installed from the Plugins menu before use. 

Will other Linux distributions from the Microsoft Store work?

Ubuntu 18.04 for Windows can also be installed to run SPAdes and Flye.  For SPAdes, Ubuntu 18.04 is only supported when using Geneious Prime 2019.2 and later.  If you wish to use Ubuntu 18.04, you’ll need to perform additional steps after installing Ubuntu and setting a username and password:

  1. Open Ubuntu 18.04 LTS from the Start menu.
  2. Install the distutils package for Python 3 with the following command, entering your Ubuntu password when prompted: 'sudo apt-get update && sudo apt-get install python3-distutils'.

Have more questions? Submit a request


  • Avatar
    Kelsey Jesser

    I've followed these directions for my Windows 10 64-bit PC, and keep getting an error message reading :


    SPAdes failed with error code 127
    /usr/bin/env: 'python': No such file or directory'

    I'm guessing this is because Spades/Geneious can't find the python installation on my computer, but I don't know how to fix this.

  • Avatar
    Geneious Team

    It appears that the Ubuntu for Windows distribution that now gets installed via the above steps has been changed recently which breaks the SPAdes plugin. We should have a work-around in the next version of Geneious. Until then, you can get it working by running these additional steps:

    1. Click on the Start menu, type 'run' and press 'Enter'
    2. In the window that shows up, type the following, including the quotes and press 'Enter' afterwards: bash -c "ln -s /usr/bin/python3 /usr/local/bin/python"

  • Avatar
    Jacob Hoyle

    Still getting the same error after running the line posted August 21st. this is in Geneious 10.2.3 and the latest windows 10

  • Avatar
    Hilary Miller

    Hi Jacob

    I can confirm that the instructions above (the main article plus the additional line you need in the comment above) work for the latest Windows 10 update (OS build 15063.726) on Geneious 10.2.

    Can you contact us via a support ticket using the Support button in Geneious, so that we can investigate why it doesn't work on your system?

  • Avatar
    Vimac Nolla Ardevol

    I'm interested in runnning SPAdes on the new Geneious Prime and before performing all the above steps would like to know if the current Ubuntu for Windows distribution is working with Geneious Prime.

  • Avatar
    Seth Cartwright

    My comment is significantly later than the last one, but I can confirm for:

    Windows 10 1903 - build 18362.476
    Ubuntu 18.04 LTS from the Microsoft Store

    I had to follow all steps in the article, plus the above Geneious Team comment about creating a link for python3 -> python

    In other words, after all article steps, run this:

    1. Click on the Start menu, type 'run' and press 'Enter'
    2. In the window that shows up, type the following, including the quotes and press 'Enter' afterwards: bash -c "ln -s /usr/bin/python3 /usr/local/bin/python"

    You can also do this inside your running Ubuntu command line instead:

    sudo bash -c "ln -s /usr/bin/python3 /usr/local/bin/python"

    This basically ties running the command "python" to your python3 installation

    Edited by Seth Cartwright