Installation - OnDemand QuPath

Instead of installing local QuPath on your laptop, we would recommend you to use OnDemand QuPath with OMERO extensions.

OnDemand (compute desktop GUI on the HPC cluster)

OnDemand is to run a virtual application on the HPC cluster. There are numerous ways to achieve this but I’m trying to offer you the current simplest method.

  • Register with IT for OnDemand usage. Once you have this you’ll be able to book a session online via this link: https://ondemand.nemo.thecrick.org/

  • Navigate to Interactive apps > Nemo Desktop

  • Adjust required settings for a desktop session:

    • Desktop environment: Xfce

    • Partition: ncpu

    • Hours: whatever long that you require to have ondemand working

    • Nodes, Tasks and Memory don’t have to be too high and I usually go with 1,1,200 respectively

    • Submit request by hitting Launch

Your job will be queued and when ready you’ll see it launchable via the ‘My Interactive Sessions’ menu. You can select reasonably high compression and low image quality as it won’t make much difference to your analysis.

To set up QuPath on demand:

  • On your local computer

    • Connect to NEMO from your local computer and set up a SENSIBLE file structure in a SENSIBLE place.

    • In this place make a directory (folder) structure something like (e.g.):

      • /camp/lab/labname/username/data

    • Avoid spaces and special characters in any names!!!

It’s a good thing to be organised at this stage. Now you can copy the unzipped QuPath into your Progs > QuPath directory. This is now accessible from OnDemand.

  • Launch your OnDemand session and you’ll get a desktop. Right click on the desktop and select Create Launcher

  • Now please follow instructions on the following link: