OMERO.server installation on CentOS 7 and Ice 3.5
=================================================
This is an example walkthrough for installing OMERO on CentOS 7, using
a dedicated system user, and should be read in conjunction with
:doc:`install-web`. 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`.
These instructions assume your Linux distribution is configured with a UTF-8
locale (this is normally the default).
For convenience in this walkthrough the main OMERO configuration options have
been defined as environment variables. When following this walkthrough you can
either use your own values, or alternatively source the following file:
.. literalinclude:: walkthrough/settings.env
:start-after: Substitute
:download:`settings.env <walkthrough/settings.env>`
Installing prerequisites
------------------------
**The following steps are run as root.**
Install Java 1.8, Ice 3.5 and PostgreSQL 9.4:
To install Java 1.8 and other dependencies:
.. literalinclude:: walkthrough/walkthrough_centos7.sh
:start-after: #start-step01
:end-before: # install Ice
To install Ice 3.5:
.. literalinclude:: walkthrough/walkthrough_centos7.sh
:start-after: #start-recommended-ice
:end-before: #end-recommended-ice
To install PostgreSQL 9.4:
.. literalinclude:: walkthrough/walkthrough_centos7.sh
:start-after: #end-supported-ice
:end-before: #end-step01
See :download:`requirements.txt<walkthrough/requirements.txt>`
Create an omero system user, and a directory for the OMERO repository:
.. literalinclude:: walkthrough/walkthrough_centos7.sh
:start-after: #start-step02
:end-before: #end-step02
Create a database user and initialize a new database for OMERO.
As postgres who is the admin for a PostgreSQL installation, run:
.. literalinclude:: walkthrough/walkthrough_centos7.sh
:start-after: #start-step03
:end-before: #end-step03
Installing OMERO.server
-----------------------
**The following steps are run as the omero system user.**
Download, unzip and configure OMERO. The rest of this walkthrough assumes the
OMERO.server is installed into the home directory of the omero system user.
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.
You will need to install the server corresponding to your Ice version.
Install ``server-ice35.zip``:
.. literalinclude:: walkthrough/walkthrough_centos6_py27_ius.sh
:start-after: #start-release-ice35
:end-before: #end-release-ice35
Configure:
.. literalinclude:: walkthrough/walkthrough_centos6_py27_ius.sh
:start-after: #end-release-ice36
:end-before: #end-step04
Installing a web server
-----------------------
To deploy OMERO.web, you can use either Nginx or Apache.
Follow the steps to install your chosen web server.
Nginx
^^^^^
See also :doc:`install-web/install-nginx`.
**The following steps are run as root.**
Install Nginx 1.8, copy the Nginx OMERO configuration file into the
Nginx configuration directory, and disable the default configuration:
.. literalinclude:: walkthrough/walkthrough_centos7.sh
:start-after: #start-nginx
:end-before: #end-nginx
See :download:`setup_omero_nginx.sh<walkthrough/setup_omero_nginx.sh>`
Apache (deprecated)
^^^^^^^^^^^^^^^^^^^
See also :doc:`install-web/install-apache`.
As the **omero** system user, configure OMERO.web:
.. literalinclude:: walkthrough/walkthrough_centos7.sh
:start-after: #start-configure-apache
:end-before: #end-configure-apache
**The following steps are run as root.**
Install Apache 2.4 and copy the Apache OMERO configuration file into the
Apache configuration directory:
.. literalinclude:: walkthrough/walkthrough_centos7.sh
:start-after: #start-apache-install
:end-before: #end-apache-install
Running OMERO
-------------
**The following steps are run as the omero system user.**
OMERO should now be set up. To start the server run::
OMERO.server/bin/omero admin start
If you deploy with Nginx, to start the OMERO.web client run::
OMERO.server/bin/omero web start
The last command is **not** necessary if you deploy with Apache.
Nginx or Apache should already be running so you should be able to log in as the OMERO
root user by going to http://localhost/ in your web browser.
Please read the SELinux_ section below.
In addition some example `systemd.service` scripts are available should you wish to
start OMERO and OMERO.web automatically:
.. literalinclude:: walkthrough/walkthrough_centos7.sh
:start-after: #start-step06
:end-before: #end-step06
| :download:`omero-systemd.service <walkthrough/omero-systemd.service>`
| :download:`omero-web-systemd.service <walkthrough/omero-web-systemd.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
Regular tasks
-------------
**The following steps are run as root.**
The default OMERO.web session handler uses temporary files to store sessions
which should be deleted at regular intervals, for instance by creating a cron
job:
.. literalinclude:: walkthrough/walkthrough_centos7.sh
:start-after: #start-omeroweb-cron
:end-before: #end-omeroweb-cron
Copy this script into the appropriate location:
.. literalinclude:: walkthrough/walkthrough_centos7.sh
:start-after: #start-copy-omeroweb-cron
:end-before: #end-copy-omeroweb-cron
| :download:`omero-web-cron <walkthrough/omero-web-cron>`
.. _SELinux_centos7:
SELinux
-------
**The following steps are run as root.**
If you are running a system with
`SELinux enabled <http://wiki.centos.org/HowTos/SELinux>`_
and are unable to access OMERO.web you may need to adjust the security policy:
.. literalinclude:: walkthrough/walkthrough_centos7.sh
:start-after: #start-selinux
:end-before: #end-selinux