OMERO.biobank installation guide

Software dependencies

Common dependencies

• Python 2.7
• OMERO Python libraries (with compiled custom models). Check out the OMERO server installation guide for a complete walkthrough on how to build OMERO server with custom models. After installation, add the Python libraries to your PYTHONPATH:

export PYTHONPATH="${OMERO_HOME}/dist/lib/python:${PYTHONPATH}"

• Ice 3.3 or 3.4 Python libraries.
• NOTE: all clients must use the same Ice version as the server
• NumPy
• biodoop-core
• NOTE: although Pydoop is listed as one of Biodoop Core's prerequisites, it's only a run-time dependency for MapReduce applications. Thus, Pydoop is currently NOT a requirement for OMERO.biobank.

With Neo4j and RabbitMQ enabled

• pika 0.9.13

pip install pika==0.9.13

• bulbs >= 0.3

pip install bulbs

• voluptuous >= 0.7.1

pip install voluptuous

With Neo4j and RabbitMQ disabled

• pygraph >= 1.8.0

easy_install python-graph-core

Configuration

Configuration parameters related to Neo4j and RabbitMQ must be retrieved from the OMERO server:

$python {BIOBANK_REPO}/build_configuration.py -H ${OMERO_HOST} -U ${OMERO_USER} -P ${OMERO_PASSWD} --python

where:

• ${OMERO_USER} must be a user with admin privileges in the OMERO server
• the --python flag sets the ${BIOBANK_REPO}/bl/vl/kb/config.py as output for the script: in this way, Neo4j and RabbitMQ config values will be installed while installing the libraries.

If you want to interact with more than one OMERO server, use --profile instead of --python: the script will produce an ${OMERO_HOST}.profile file that can be sourced to load config values as environment variables.

Installation

System-wide:

sudo ${BIOBANK_REPO}/setup.py install

Local (i.e., into ~/.local/lib/python2.7/site-packages):

${BIOBANK_REPO}/setup.py install --user