Linux Install Walkthrough

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.

Debian 6.0

Zeroc Ice Version:

• 3.3

Omero Versions:

• 4.3.x Release
• 4.4 Develop

Ubuntu 10.04 (LTS) - Ubuntu 11.04

Zeroc Ice Version:

• 3.3

Omero Versions:

• 4.3.x Release
• 4.4 Develop

Ubuntu 11.10

Zeroc Ice Version:

• 3.4

Omero Versions:

• 4.4 Develop

NB 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 targetting.

Prerequisites: The Base Software Install

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

First we need to enable the contrib & Non-Free repositories by opening /etc/apt/sources.list in an editor, e.g. $ sudo vim /etc/apt/sources.list & 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

NB. For Ubuntu the repository names & locations are different to Debian but you need to enable the main, restricted, universe & 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 we need to update our package lists to ensure that we get the latest packages including those from the repositories that we just enabled:

  $ sudo apt-get update

Oracle recently changed their distribution license (OSDL) which means that Debian & Ubuntu can no longer distribute Java in their package management systems. This means that we have to install the JDK separately as follows:

If you are on Debian then:

  $ sudo apt-get install lsb_release

For both Debian & 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

Now we are ready to install the rest of our 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

NB. On Ubuntu some of the packages are slightly different & do not necessarily install ALL of the same software as Debian. For example, python-tables on Ubuntu does not install . As a result, on Ubuntu we may also need to install liblzo otherwise OMERO.tables will fail to start:

  $ sudo apt-get install liblzo2-2

We also need to ensure that the Sun/Oracle JDK is the active one as we 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.

Setup Environment

Edit your .bashrc file, e.g. $ vim ~/.bashrc and add the following (NB - you may wish to check postgres and python versions by checking the directories themselves, since they may not correspond to those listed below). In particular check the version of python that is installed. Newer versions of Ubuntu are installing python2.7 by default now from APT:

  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_HOME=~/apps/OMERO/OMERO.server
  export PATH=$PATH:$JAVA_HOME/bin:$ICE_HOME:$POSTGRES_HOME/bin:$OMERO_HOME/bin
  export PYTHONPATH=/usr/lib/pymodules/python2.6:$PYTHONPATH
  export LD_LIBRARY_PATH=/usr/share/java:/usr/lib:$LD_LIBRARY_PATH

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

  $ source ~/.bashrc

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

  $ echo $OMERO_HOME

should give output similar to the following:

  ~/apps/OMERO/OMERO.server

Configure Software

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

  U: omerouser 
  P: omeropass
  DB: omerodb

NB. 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 outwith the scope of this document

Setup postgresql:

  $ sudo -u postgres createuser -P -D -R -S omerouser
  $ sudo -u postgres createdb -O omerouser omerodb
  $ sudo -u postgres createlang plpgsql omerodb

NB. Check that a database called "omerodb" has been created:

  $ psql -h localhost -U omerouser -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

_NB. The backslash '' in the sed command above is used merely to indicate a line-break & 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 postgre 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

Install OMERO.server

Now that all of the prerequisites are installed & configured we can get to the important business of setting up the OMERO.server. First we need to create a home for our server and move into that directory. I like to install certain software, such as OMERO, locally into a directory called apps in my home directory as follows:

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

NB. Recall that earlier we set the OMERO_HOME environment variable to ~/apps/OMERO/OMERO.server. If you change the location that you wish to install OMERO to then you will also have to alter your OMERO_HOME environment variable to reflect this.

Release versions of OMERO.server can downloaded from http://cvs.openmicroscopy.org.uk/snapshots/omero/ where the current release, at time of writing, is 4.3.4

  $ wget http://cvs.openmicroscopy.org.uk/snapshots/omero/OMERO.server-Beta-4.3.4.zip

NB. If you want the development version of OMERO.server which is currently version 4.4 then you can clone the src code from the project's GitHub account at https://github.com/openmicroscopy/openmicroscopy to build locally or download a daily build from our build server http://hudson.openmicroscopy.org.uk/job/OMERO-trunk/lastSuccessfulBuild/artifact/

Assuming that you downloaded a release version of OMERO.server, extract it from the zip archive:

  $ unzip OMERO.server-Beta-4.3.1.zip

Give your OMERO software install a nice local name to save some typing later, to reflect what we set OMERO_HOME to, & to make it easy to manage the installation of newer versions of the server at a later date:

  $ ln -s OMERO.server-Beta-4.3.1 OMERO.server

Configure OMERO.server

Now we can configure OMERO.server so that it can connect to the postgres database:

  $ omero config set omero.db.name 'omerodb'
  $ omero config set omero.db.user 'omerouser'
  $ omero config set omero.db.pass 'omeropass'

NB. 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, I like to keep mine in ~/apps/OMERO/OMERO.data so, within ~/apps/OMERO/ use the following command:

  $ mkdir OMERO.data

Configure OMERO to find the data location:

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

We can now configure the empty Postgres 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. "omeropass"

  $ omero db script

The output of this should be a file named, e.g. OMERO4.30.sql file in your current directory. We can now tell Postgres to configure our new database

  $ psql -h localhost -U omerouser omerodb < OMERO4.3__0.sql

At this point your should see a whole load of output from Postgres 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: omero

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

  $ omero config set omero.web.application_server development
  $ omero web start

Now you should be able to connect on the same machine with:

  http://localhost:4080/webadmin
  http://localhost:4080/webclient