Installing OMERO from source

Using the source code

The source code of each release of OMERO is available for download from the Source code section of the OMERO download page.

Note

At the moment, this source code bundle does not contain the version of Bio-Formats. To include this version information, you will need to manually copy the ant/gitversion.xml file included in the source code bundle of Bio-Formats for the same release under components/bioformats/ant.

Using the Git source repository

To use the Git source repository, you will need to install Git on your system. See the Using Git section of the Contributing documentation for more information on how to install and configure Git.

The main repository for OMERO is available from https://github.com/openmicroscopy/openmicroscopy. Most OME development is currently happening on GitHub, therefore it is highly suggested that you become familiar with how it works, if not create an account for yourself.

Start by cloning the official repository:

git clone https://github.com/openmicroscopy/openmicroscopy.git

Since the openmicroscopy repository now makes use of submodules, you first need to initialize all the submodules:

cd openmicroscopy
git submodule update --init

Alternatively, with version 1.6.5 of git and later, you can pass the --recursive option to git clone and initialize all submodules:

git clone --recursive https://github.com/openmicroscopy/openmicroscopy.git

See also

Using Git

Section of the contributing documentation explaining how to use Git for contributing to the source code.

Building OMERO

To install the dependencies required to run the OMERO.server on Linux or Mac OS X, take a look at the OMERO.server installation or the OMERO.server Mac OS X installation walk-through with Homebrew sections.

Additional dependencies are necessary for building the server and clients:

• Genshi can be installed using either the package manager or Python packaging tools such as easy_install or pip:

  pip install Genshi
  

• Ice Python and Java development packages may need to be explicitly installed on Linux.

Finally, some environment variables may need to be set up before building the server:

• If the system slice files cannot be found you must set SLICEPATH to point to the slice directory of the Ice installation.

For example, on CentOS 6 the following should be sufficient to run the default build:

yum install java-1.7.0-openjdk-devel python-genshi python-setuptools \
    ice-servers ice-python-devel ice-java-devel ice-c++-devel

export SLICEPATH=/usr/share/Ice-3.5.1/slice

On Ubuntu 14.04:

apt-get install openjdk-7-jdk python-genshi python-setuptools zeroc-ice

Once all the dependencies and environment variables are set up, you can build the server using:

python build.py

or the clients using:

python build.py release-clients

See also

Build System

Section of the developer documentation detailing the build system