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 Windows Subsystem for Linux, following the setup instructions below.  You must have installed all recent updates for Windows 10.

Setup instructions to run SPAdes 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). Close Ubuntu.
  7. 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').

Will SPAdes work with other Linux distributions from the Microsoft Store?

The Microsoft Store now offers multiple Linux distributions for Windows 10, however, SPAdes in Geneious is only supported on Ubuntu 16.04 (recommended, Geneious 10.1 and greater) and 18.04 (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'.

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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.