OMERO.server installation on Ubuntu 16.04

This is an example walkthrough for installing OMERO on Ubuntu, using a dedicated system user, and should be read in conjunction with OMERO.web administration. You can use this as a guide for setting up your own test server. For production use you should also read the pages listed under Optimizing Server Configuration.

This guide describes how to install the recommended versions, not all the supported versions. This should be read in conjunction with Version requirements.

This guide does not describe how to install OMERO.web. To deploy OMERO.web separately from OMERO.server (recommended), please read OMERO.web installation separately from OMERO.server on Ubuntu 16.04 and IcePy 3.6 or to deploy with OMERO.server OMERO.web installation with OMERO.server on Ubuntu 16.04 and IcePy 3.6

These instructions assume your Linux distribution is configured with a UTF-8 locale (this is normally the default).

For convenience in this walkthrough the main OMERO configuration options have been defined as environment variables. When following this walkthrough you can either use your own values, or alternatively source settings.env:

OMERO_DB_USER=db_user
OMERO_DB_PASS=db_password
OMERO_DB_NAME=omero_database
OMERO_ROOT_PASS=omero_root_password
OMERO_DATA_DIR=/OMERO


export OMERO_DB_USER OMERO_DB_PASS OMERO_DB_NAME OMERO_ROOT_PASS OMERO_DATA_DIR

export PGPASSWORD="$OMERO_DB_PASS"

Installing prerequisites

The following steps are run as root.

Install Java 1.8, Ice 3.6 and PostgreSQL 9.6:

To install Java 1.8 and other dependencies:

apt-get update

# installed for convenience
apt-get -y install unzip wget bc

# install Java
apt-get -y install software-properties-common
add-apt-repository -y ppa:openjdk-r/ppa
apt-get update
apt-get -y install openjdk-8-jre

# install dependencies

apt-get update
apt-get -y install \
	unzip \
	wget \
	python-{pip,tables,virtualenv,yaml,jinja2}

pip install --upgrade pip

To install Ice 3.6:

apt-get -y install db5.3-util
apt-get -y install libssl-dev libbz2-dev libmcpp-dev libdb++-dev libdb-dev

apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 5E6DA83306132997
apt-add-repository "deb http://zeroc.com/download/apt/ubuntu`lsb_release -rs` stable main"
apt-get update
apt-get -y install zeroc-ice-all-runtime zeroc-ice-all-dev

pip install "zeroc-ice>3.5,<3.7"

To install PostgreSQL 9.6:

# install Postgres
apt-get -y install apt-transport-https
add-apt-repository -y "deb https://apt.postgresql.org/pub/repos/apt/ xenial-pgdg main 9.6"
wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add -
apt-get update
apt-get -y install postgresql-9.6
service postgresql start

Create an omero system user, and a directory for the OMERO repository:

useradd -m omero
chmod a+X ~omero

mkdir -p "$OMERO_DATA_DIR"
chown omero "$OMERO_DATA_DIR"

Create a database user and initialize a new database for OMERO:

echo "CREATE USER $OMERO_DB_USER PASSWORD '$OMERO_DB_PASS'" | su - postgres -c psql
su - postgres -c "createdb -E UTF8 -O '$OMERO_DB_USER' '$OMERO_DB_NAME'"

psql -P pager=off -h localhost -U "$OMERO_DB_USER" -l

Installing OMERO.server

The following steps are run as the omero system user.

Download, unzip and configure OMERO. The rest of this walkthrough assumes the OMERO.server is installed into the home directory of the omero system user.

Note that this script requires the same environment variables that were set earlier in settings.env, so you may need to copy and/or source this file as the omero user.

You will need to install the server corresponding to your Ice version.

Install server-ice36.zip:

cd ~omero
SERVER=https://downloads.openmicroscopy.org/latest/omero5/server-ice36.zip
wget $SERVER -O OMERO.server-ice36.zip
unzip -q OMERO.server*

Configure:

ln -s OMERO.server-*/ OMERO.server
OMERO.server/bin/omero config set omero.data.dir "$OMERO_DATA_DIR"
OMERO.server/bin/omero config set omero.db.name "$OMERO_DB_NAME"
OMERO.server/bin/omero config set omero.db.user "$OMERO_DB_USER"
OMERO.server/bin/omero config set omero.db.pass "$OMERO_DB_PASS"
OMERO.server/bin/omero db script -f OMERO.server/db.sql --password "$OMERO_ROOT_PASS"
psql -h localhost -U "$OMERO_DB_USER" "$OMERO_DB_NAME" < OMERO.server/db.sql

Running OMERO.server

The following steps are run as the omero system user.

OMERO should now be set up. To start the server run:

OMERO.server/bin/omero admin start

In addition omero-init.d is available should you wish to start OMERO automatically.

Securing OMERO

The following steps are run as root.

If multiple users have access to the machine running OMERO you should restrict access to OMERO.server’s configuration and runtime directories, and optionally the OMERO data directory:

chmod go-rwx OMERO.server/etc OMERO.server/var

# Optionally restrict access to the OMERO data directory
# chmod go-rwx "$OMERO_DATA_DIR"