How do I set up Windows 10 to run SPAdes Genome Assembler?

SPAdes (St. Petersburg genome assembler) is a de novo assembler, intended for assembling small genomes, including standard isolates and single-cell MDA bacteria assemblies.  SPAdes is available in Geneious R10.1 and later.

Normally SPAdes can only run on a 64-bit Linux system or Mac OS, but within Geneious it is possible to run SPAdes on a 64-bit Windows 10 system if you install some additional Windows features, following the setup instructions below.  You must have installed all recent updates for Windows 10.

Setup instructions to run SPAdes on Windows 10

  1. Open Settings -> Updates & Security -> For Developers (or click on the Start menu, type 'developer features' and press 'Enter')
  2. Toggle the option to turn on 'Developer Mode', wait for the Developer Mode package to install and close the Settings window
  3. Open Windows Features – click on the Start menu, type 'windows features' and press 'Enter'
  4. Tick the checkbox for 'Windows Subsystem for Linux (Beta)' and click 'OK'
  5. Restart your computer if Windows prompts you to do so
  6. Open the 'Run' app by pressing the 'Windows' and the 'R' keys at the same time, or by clicking on the Start menu, typing 'run' and pressing 'Enter'
  7. In the window that shows up, type 'lxrun /install /y' and press 'Enter' (make sure to include the spaces, but don't include the quote marks)
  8. Wait until the installation window disappears (this may take a few minutes)
  9. You should now be able to run SPAdes on your Windows 10 machine (until you have run SPAdes for the first time the message about setting this up will still show, but it should now run if you click 'OK')

What do these instructions actually do and why?

In the current version of Windows 10, a Linux distribution 'Ubuntu for Windows' can be installed. Following the instructions above will instruct your computer to download and install 'Ubuntu for Windows' from the Windows Store. Once installed, Geneious can then run SPAdes within 'Ubuntu for Windows' for you, so that you can use SPAdes easily as a standard Geneious operation.  

To install 'Ubuntu for Windows' it is necessary to turn on 'Developer Mode'. For an explanation of 'Developer Mode' you may wish to review Microsoft's article Enable your device for developmentMore information on installing 'Ubuntu for Windows' can be found in Microsoft's Installation Guide.

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  • 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.