Note
This documentation is for the new OMERO 5.3 version. See the latest OMERO 5.2.x version or the previous versions page to find documentation for the OMERO version you are using if you have not upgraded yet.
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.
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 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.