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.
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.
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
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.
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
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
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-rc1-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-rc1-ice33-byy OMERO.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
Alternatively, you can download a daily build of the OMERO.server from our continuous integration server.
Warning
The OMERO_HOME environment variable is used internally by OMERO. Unless you really know what you are doing, it is strongly recommended not to set this variable.
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
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
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
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.