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OMERO.server installation on CentOS 7

This is an example walkthrough for installing OMERO on CentOS 7, 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 3.6. 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-centos7-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 |postgresversion|:

To install Java |javaversion_recommended| and other dependencies:

.. literalinclude:: walkthrough/walkthrough_centos7.sh
    :start-after: #start-step01
    :end-before: #end-step01

To install Ice |iceversion|:

.. literalinclude:: walkthrough/walkthrough_centos7.sh
    :start-after: #start-recommended-ice
    :end-before: #end-recommended-ice

To install PostgreSQL |postgresversion|:

.. literalinclude:: walkthrough/walkthrough_centos7.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_centos7_pg_deps.sh

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

.. literalinclude:: walkthrough/walkthrough_centos7.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_centos7.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_centos7.sh
    :start-after: #start-step03bis
    :end-before: #end-step03bis

Download and unzip OMERO.server:

.. literalinclude:: walkthrough/walkthrough_centos7.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_centos7.sh
    :start-after: #end-release-ice36
    :end-before: #end-step04-pre

Configuring 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_centos7.sh
    :start-after: #end-copy-omeroscript
    :end-before: #end-step04


.. literalinclude:: walkthrough/walkthrough_centos7.sh
    :start-after: #start-seclevel
    :end-before: #end-seclevel

See also :doc:`../client-server-ssl`.

Running 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_centos7.sh
    :start-after: #start-step06
    :end-before: #end-step06

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_centos7.sh
    :start-after: #start-step07
    :end-before: #end-step07