Migration from OMERO 5.2 on Windows to OMERO 5.3 on Linux

Backup (Windows)

  • Create a dump of the OMERO SQL database, either using pgAdmin or the pg_dump command line program:

    pg_dump -Fc -f omero52.pg_dump omero_database
  • Please keep a pristine copy of your Windows OMERO server, until you are sure that the new 5.3 installation works flawlessly. That means if you use a network storage system for hosting the binary data store, back it up before mounting it onto the new Linux system.

  • Save custom configuration properties which might have been set:

    omero config get > omero.config
  • For more details on the standard backup procedure, see OMERO.server backup and restore.

Install OMERO 5.3 (Linux)

Follow the OMERO.server installation overview documentation to install OMERO 5.3 on your Linux system, until (including) step 3 of the Configuration part (setting the binary repository location).

There is no need to generate the database initialization script, as you are going to use the previously generated database backup from your old 5.2 server installation.

Restore Data (Linux)

  • Restore the 5.2 database dump:

    sudo -u postgres pg_restore -Fc -d omero_database omero52.pg_dump
  • Upgrade the database to 5.3 following the Upgrade your database documentation

  • Adjust the paths stored in the database from Windows style to Unix style, e. g. using psql command line:

    UPDATE pixels SET path = regexp_replace(path,'\\','/','g');
  • Copy the binary data store from your Windows system (e.g. C:\OMERO) over to the Linux system (e.g. /OMERO), or if you use a network storage system then mount it onto the Linux system (make sure you have a backup beforehand)

  • Restore custom configuration properties (see Backup step 3):

    omero config load omero.config

Finally start the OMERO server and check the log files for errors.