.. walkthroughs are generated using a bash script, see
.. https://github.com/ome/omero-install

OMERO.server installation on RHEL 9/Rocky Linux 9
=================================================

This is an example walkthrough for installing OMERO on RHEL 9/Rocky Linux 9, 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 :ref:`index-optimizing-server`.
This guide will install Python 3.9.
Since 5.6, a new :envvar:`OMERODIR` variable is used, you should first unset :envvar:`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 :doc:`../version-requirements`.

This guide **does not** describe how to install OMERO.web.
To deploy OMERO.web, please read
:doc:`install-web/walkthrough/omeroweb-install-rockylinux9-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 :file:`settings.env` for example under ``/tmp`` e.g. ``/tmp/settings.env`` containing the variables below and source it when required:

.. literalinclude:: walkthrough/settings.env
   :start-after: Substitute

Installing prerequisites
------------------------

**The following steps are run as root.**

Install Java |javaversion_recommended|, Ice |iceversion| and PostgreSQL 16:

To install Java |javaversion_recommended| and other dependencies:

.. literalinclude:: walkthrough/walkthrough_rocky9.sh
    :start-after: # install Java
    :end-before: #end-step01

To install Ice |iceversion|:

.. literalinclude:: walkthrough/walkthrough_rocky9.sh
    :start-after: #start-recommended-ice
    :end-before: #end-recommended-ice

To install PostgreSQL:

.. literalinclude:: walkthrough/walkthrough_rocky9.sh
    :start-after: # install Postgres
    :end-before: #end-step01

.. Note:: if you are installing PostgreSQL in a Docker container, some of the commands above will not work. For more details check `step01_rocky9_deps.sh 
 <https://github.com/ome/omero-install/blob/develop/linux/step01_rocky9_deps.sh>`_

Create a local omero-server system user, and a directory for the OMERO repository:

.. literalinclude:: walkthrough/walkthrough_rocky9.sh
    :start-after: #start-step02
    :end-before: #end-step02

Make the :file:`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:

.. literalinclude:: walkthrough/walkthrough_rocky9.sh
    :start-after: #start-step03
    :end-before: #end-step03

Installing OMERO.server
-----------------------

**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``:

.. literalinclude:: walkthrough/walkthrough_rocky9.sh
    :start-after: #start-step03bis
    :end-before: #end-step03bis

Download and unzip OMERO.server:

.. literalinclude:: walkthrough/walkthrough_rocky9.sh
    :start-after: #start-release-ice36
    :end-before: #end-release-ice36

Change the ownership of the OMERO.server directory and create a symlink:

.. literalinclude:: walkthrough/walkthrough_rocky9.sh
    :start-after: #end-release-ice36
    :end-before: #end-step04-pre

Configuring the OMERO.server
----------------------------

**The following steps are run as the omero-server system user.** (``su - omero-server``)

The variable ``OMERODIR`` set in :download:`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:

.. literalinclude:: walkthrough/walkthrough_rocky9.sh
    :start-after: #end-copy-omeroscript
    :end-before: #end-step04

.. include:: ciphers

.. literalinclude:: walkthrough/walkthrough_rocky9.sh
    :start-after: #start-seclevel
    :end-before: #end-seclevel

Running the OMERO.server
------------------------

**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 start

Should you wish to start OMERO automatically, a `systemd service file` could be created.
An example :download:`omero-server-systemd.service <walkthrough/omero-server-systemd.service>`
is available.

Copy the ``systemd.service`` file and configure the service:

.. literalinclude:: walkthrough/walkthrough_rocky9.sh
    :start-after: #start-step08
    :end-before: #end-step08

You can then start up the service.

Securing OMERO
--------------

**The 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:

.. literalinclude:: walkthrough/walkthrough_rocky9.sh
    :start-after: #start-step07
    :end-before: #end-step07
