This is an example walkthrough for installing OMERO on Ubuntu 22.04, using a dedicated local system user. You can use this as a guide for setting up your own test server. For production use you should also read the pages listed under index-optimizing-server. This guide will install Python 3.10. Since 5.6, a new OMERODIR variable is used, you should first unset OMERO_HOME (if set) before beginning the installation process.
This guide describes how to install using the recommended versions for Java, Ice, PostgreSQL. This should be read in conjunction with ../version-requirements.
This guide does not describe how to install OMERO.web. To deploy OMERO.web, please read install-web/walkthrough/omeroweb-install-ubuntu2204-ice3.6.
These instructions assume your Linux distribution is configured with a UTF-8 locale (this is normally the default).
For convenience in this walkthrough we will use the omero-server system user and the main OMERO configuration options have been defined as environment variables. When following this walkthrough you can either use your own values, or alternatively create settings.env for example under /tmp e.g. /tmp/settings.env containing the variables below and source it when required:
walkthrough/settings.env
The following steps are run as root.
Install Java , Ice and PostgreSQL :
To install Java and other dependencies:
walkthrough/walkthrough_ubuntu2204.sh
To install Ice :
walkthrough/walkthrough_ubuntu2204.sh
To make Ice available to all users and activate the virtual environment, set the following in /etc/profile:
walkthrough/omero-ice36.env
and add the virtual environment to PATH:
walkthrough/settings.env
To install PostgreSQL:
walkthrough/walkthrough_ubuntu2204.sh
Create a local omero-server system user, and a directory for the OMERO repository:
walkthrough/walkthrough_ubuntu2204.sh
Make the settings.env available to the omero-server system user by copying in to the user home directory. The file will need to be sourced each time you switch user. You could add . ~/settings.env to the omero-server system user bash profile.
Create a database user and initialize a new database for OMERO:
walkthrough/walkthrough_ubuntu2204.sh
The following step is run as root.
We recommend to create a virtual environment and install the Ice Python binding and the dependencies required by the server using pip:
walkthrough/walkthrough_ubuntu2204.sh
Download and unzip OMERO.server:
walkthrough/walkthrough_ubuntu2204.sh
Change the ownership of the OMERO.server directory and create a symlink:
walkthrough/walkthrough_ubuntu2204.sh
The following steps are run as the omero-server system user. (su - omero-server)
The variable OMERODIR set in settings.env <walkthrough/settings.env> above must point to the location where OMERO.server is installed. e.g. OMERODIR=/path_to_omero_server/OMERO.server.
Note that this script requires the same environment variables that were set earlier in settings.env, so you may need to copy and/or source this file as the omero user.
Configure the database and the location of the data directory:
walkthrough/walkthrough_ubuntu2204.sh
walkthrough/walkthrough_ubuntu2204.sh
See also ../client-server-ssl.
The following steps are run as the omero-server system user. (su - omero-server)
OMERO should now be set up. To start the server run:
omero admin startShould you wish to start OMERO automatically, a init.d file could be created. An example omero-server-init.d <walkthrough/omero-server-init.d> is available.
Copy the init.d file and configure the service:
walkthrough/walkthrough_ubuntu2204.sh
You can then start up the service by running:
service omero-server startThe following steps are run as root.
If multiple users have access to the machine running OMERO you should restrict access to OMERO.server's configuration and runtime directories, and optionally the OMERO data directory:
walkthrough/walkthrough_ubuntu2204.sh