OMERO.scripts are the OME version of plugins, allowing you to extend the functionality of OMERO. Official core OMERO.scripts come bundled with every OMERO.server release but you can also add new scripts you have written yourself or found via the repositories forked from ome/omero-user-scripts.


Uploading and managing scripts

OMERO.scripts user guide describes the workflow for developing and uploading scripts as an Admin. Any scripts you add to the lib/scripts/ directory as a server admin will be considered ‘trusted’ and automatically detected by OMERO, allowing them to be run on the server from the clients or command line by any of your users.

Once in the directory, scripts cannot be automatically updated and any additional ones will be lost when you upgrade your server installation. Therefore, we recommend you use a Github repository to manage your scripts. If you are not familiar with using git, you can use the GitHub app for your OS (available for Mac and Windows but not Linux). The basic workflow is:

  • fork our omero-user-script repository

  • clone it in your lib/scripts directory

    cd lib/scripts;
    git clone YOUR_SCRIPTS
  • save the scripts you want to use into the appropriate sub-directory in your cloned location lib/scripts/YOUR_SCRIPTS

Then when you upgrade your OMERO.server installation, provided your Github repository is up to date with all your latest script versions (i.e. all your local changes are committed), you just need to repeat the git clone step. Those scripts will then be automatically detected by your new server installation and available for use from the clients and command line as before.