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OMERO.server Linux installation walk-through

This page walks through the process of installing OMERO.server on a machine using a Debian-based Linux distribution.

Note

This page is generally applicable to Debian and Ubuntu installations, although there are some small differences which are noted when applicable during the walk-through.

Distributions

Whilst OMERO can be made to work on a wide range of Linux distributions, installation using a package manager is the most straightforward way to get an OMERO installation up and running. However, due to changes between releases of Ubuntu and Debian, there are some restrictions over which version of OMERO can be easily installed using the package manager to install and manage the OMERO prerequisites.

Distribution ZeroC Ice version OMERO version
Debian 7.0 3.4 4.4.x
Debian 6.0 3.3 4.3.x, 4.4.x
Ubuntu 12.04 (LTS) 3.4 4.4.x
Ubuntu 11.10 3.4 4.4.x
Ubuntu 11.04 3.3 4.3.x, 4.4.x
Ubuntu 10.04 (LTS) 3.3 4.3.x, 4.4.x

Note

ZeroC Ice can always be built from source code for specific platforms.

In the remainder of this guide you should adjust version numbers to suit the distribution that you are targeting.

Prerequisites

You require at least a clean minimal Debian or Ubuntu installation and a non-root user account that has sudo privileges.

First you need to enable the contrib and non-free repositories by opening /etc/apt/sources.list in an editor, e.g. $ sudo vim /etc/apt/sources.list and editing to add the following lines:

deb http://ftp.uk.debian.org/debian/ squeeze contrib
deb-src http://ftp.uk.debian.org/debian/ squeeze contrib

deb http://ftp.uk.debian.org/debian/ squeeze non-free
deb-src http://ftp.uk.debian.org/debian/ squeeze non-free

Note

For Ubuntu the repository names and locations are different to Debian but you need to enable the main, restricted, universe and multiverse repositories. You can do this either by editing /etc/apt/sources.list directly, in which case the entries already exist but are commented out, or using Synaptic (10.04 & 10.10) or Ubuntu Software Center (11.04 onwards).

Now you need to update your package lists to ensure that you get the latest packages including those from the repositories that you just enabled:

$ sudo apt-get update

Java

From Ubuntu 11.10 and onwards, you can install OpenJDK 7 using:

$ sudo apt-get install openjdk-7-jdk

For earlier versions of Ubuntu, Oracle recently changed their distribution license (OSDL) which means that Debian and Ubuntu can no longer distribute Java in their package management systems. This means that you have to install the JDK separately as follows:

If you are on Debian then:

$ sudo apt-get install lsb_release

For both Debian and Ubuntu you can now:

$ sudo apt-get install git
$ git clone https://github.com/flexiondotorg/oab-java6.git
$ cd oab-java6/
$ sudo ./oab-java6.sh

The script will run and you should see some output indicating progress. When you get your prompt back:

$ sudo apt-get install sun-java6-jdk

You also need to ensure that the Sun/Oracle JDK is the active one as you end up with the OpenJDK also installed to satisfy dependencies along the way:

$ sudo update-alternatives --config java

and select the correct java from the displayed list.

OMERO dependencies

Now you are ready to install the rest of your prerequisite software packages:

$ sudo apt-get install unzip build-essential mencoder
$ sudo apt-get install python python-imaging python-numpy python-tables python-matplotlib
$ sudo apt-get install zeroc-ice33
$ sudo apt-get install postgresql
$ sudo apt-get install apache2 libapache2-mod-fastcgi

Note

On Ubuntu 11.04 and earlier, python-tables does not install. You need to install liblzo otherwise OMERO.tables will fail to start:

$ sudo apt-get install liblzo2-2

OMERO installation

Once the prerequisites are installed and configured, the OMERO.server can be set up. First, a home needs to be created for the server and this directory moved into. For example, to install OMERO locally into a directory called ‘apps’ in your home directory, use the following:

$ mkdir apps
$ cd apps
$ mkdir OMERO
$ cd OMERO

OMERO 5.0.0

Release versions of OMERO.server can downloaded from the OMERO downloads page. Assuming that you downloaded a release version of OMERO.server, extract it from the zip archive:

$ unzip OMERO.server-5.0.0-ice33-byy.zip

Give your OMERO software install a nice local name to save some typing later, to reflect what you set OMERO_PREFIX to in the Configuration section, and to make it easy to manage the installation of newer versions of the server at a later date:

$ ln -s OMERO.server-5.0.0-ice33-byy  OMERO.server

Development server

If you want the development version of OMERO.server, you can clone the source code from the project’s GitHub account to build locally:

$ git clone --recursive git://github.com/openmicroscopy/openmicroscopy
$ cd openmicroscopy && ./build.py

Note

If you have a GitHub account and you plan to develop code for OMERO, you should make a fork into your own account and then clone this fork to your local development machine, e.g.

$ git clone --recursive git://github.com/YOURNAMEHERE/openmicroscopy
$ cd openmicroscopy && ./build.py

See also

Installing OMERO from source
Developer documentation page on how to check out to source code
Build System
Developer documentation page on how to build the OMERO.server

Alternatively, you can download a daily build of the OMERO.server from our continuous integration server.

Configuration

Environment variables

Warning

The OMERO_HOME environment variable is used internally by OMERO. Unless you really know what you are doing, it is strongly recommended that you do not set this variable (see Setting the OMERO_HOME environment variable for details). You can use a different name of your choice instead, indicated by OMERO_PREFIX in this documentation.

Edit your .bashrc file, e.g. $ vim ~/.bashrc and add the following:

export JAVA_HOME=/usr/lib/jvm/java-6-sun
export ICE_HOME=/usr/share/Ice-3.3.1
export POSTGRES_HOME=/usr/lib/postgresql/8.4
export OMERO_PREFIX=~/apps/OMERO/OMERO.server
export PATH=$PATH:$JAVA_HOME/bin:$ICE_HOME:$POSTGRES_HOME/bin:$OMERO_PREFIX/bin
export PYTHONPATH=/usr/lib/pymodules/python2.6:$PYTHONPATH
export LD_LIBRARY_PATH=/usr/share/java:/usr/lib:$LD_LIBRARY_PATH

Note

You may wish to check PostgreSQL and Python versions by checking the directories themselves, since they may not correspond to those listed above. In particular check the version of Python that is installed. Newer versions of Ubuntu are installing Python 2.7 from APT by default.

Now you need to make those changes take effect by getting your shell to apply them using the source built-in command:

$ source ~/.bashrc

You can check that the new environment variables have taken by printing their values to the shell, e.g.:

$ echo $OMERO_PREFIX
/home/ome/apps/OMERO/OMERO.server

Database creation

Now you need to configure your prerequisites so that they are ready for OMERO to make use of. For the purposes of this walk-through you can use the following dummy data for the user account:

U: db_user
P: db_password
DB: omero_database

Note

For a live or public server install these values should be altered to reflect your security requirements. You should also consider locking down your server machine but that is outside the scope of this document.

Set up PostgreSQL:

$ sudo -u postgres createuser -P -D -R -S db_user
$ sudo -u postgres createdb -O db_user omero_database
$ sudo -u postgres createlang plpgsql omero_database

Check that a database called “omerodb” has been created:

$ psql -h localhost -U db_user -l

Update PostgreSQL host-based authentication to accept remote connections:

$ sudo sed '/127.0.0.1/s/md5/trust/' /etc/postgresql/8.4/main/pg_hba.conf \
    > pg_hba.conf && sudo mv pg_hba.conf /etc/postgresql/8.4/main/pg_hba.conf

Note

The backslash ‘\’ in the sed command above is used merely to indicate a line-break and should not be included in the executed command

Restart PostgreSQL:

$ sudo /etc/init.d/postgresql restart

Use netstat to verify that there is something listening on port 5432, this should be your PostgreSQL server:

$ netstat -an | egrep '5432.*LISTEN'

which should display a line similar to the following:

tcp        0      0 127.0.0.1:5432          0.0.0.0:*               LISTEN

OMERO.server

Now you can configure OMERO.server so that it can connect to the PostgreSQL database:

$ omero config set omero.db.name 'omero_database'
$ omero config set omero.db.user 'db_user'
$ omero config set omero.db.pass 'db_password'

Note

If you altered any of these values earlier then you will need to change them to reflect your requirements

You can also check the values that have been set using:

$ omero config get

Create a home for your OMERO data. For example, to install the OMERO data locally into ~/apps/OMERO/OMERO.data, use the following command:

$ mkdir ~/apps/OMERO/OMERO.data

Configure OMERO to find the data location:

$ omero config set omero.data.dir ~/apps/OMERO/OMERO.data

You can now configure the empty PostgreSQL database using Omero’s db script. You can accept the defaults for the first few values and enter a suitable password as required when prompted, e.g. “root_password:

$ omero db script

The output of this should be a file named, e.g. OMERO5.0__0.sql file in your current directory. You can now tell PostgreSQL to configure your new database

$ psql -h localhost -U db_user omero_database < OMERO5.0__0.sql

At this point you should see a whole load of output from PostgreSQL as it installs the new OMERO database.

If all has gone well, you should now be able to start OMERO.server using the following command:

$ omero admin start

You should now be able to connect to your OMERO.server using an OMERO client such as OMERO.insight and the following credentials:

U: root
P: root_password

OMERO.web

To connect with the webclient or webadmin using the included Django development server:

$ omero config set omero.web.application_server development
$ omero config set omero.web.debug True

You should be able to start the Web server with:

$ omero web start
Starting django development webserver...
Validating models...
0 errors found

Django version 1.1.1, using settings 'omeroweb.settings'
Development server is running at http://0.0.0.0:4080/
Quit the server with CONTROL-C.