OMERO.server installation on Ubuntu 16.04

This is an example walkthrough for installing OMERO on Ubuntu 16.04, 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 will install Python 3.5.

This guide describes how to install using the recommended versions for Java, Ice, PostgreSQL. This should be read in conjunction with Version requirements.

This guide does not describe how to install OMERO.web. To deploy OMERO.web, please read OMERO.web installation 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 we will use the omero system user and 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
# Location of the OMERO.server
OMERODIR=/opt/omero/server/OMERO.server
# Location of the virtual environment for omero-py
VENV_SERVER=/opt/omero/server/venv3


export OMERO_DB_USER OMERO_DB_PASS OMERO_DB_NAME OMERO_ROOT_PASS OMERO_DATA_DIR

export PGPASSWORD="$OMERO_DB_PASS"

export OMERODIR
PATH=$VENV_SERVER/bin:$PATH
export PATH

Installing prerequisites

The following steps are run as root.

Install Java 11, Ice 3.6.5 and PostgreSQL 11:

To install Java 11 and other dependencies:

apt-get update

apt-get -y install unzip wget bc

# to be installed if daily cron tasks are configured
apt-get -y install cron

# install Java
apt-get -y install software-properties-common
add-apt-repository ppa:openjdk-r/ppa
apt-get update -q
apt-get install -y openjdk-11-jre

# install dependencies
apt-get update
apt-get -y install \
	unzip \
	wget \
	python3 \
	python3-venv

# to be installed if recommended/suggested is false
apt-get -y install python3-setuptools python3-wheel

To install Ice 3.6.5:

apt-get -y install software-properties-common
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

To install PostgreSQL 11:

apt-get -y install apt-transport-https
add-apt-repository -y "deb https://apt.postgresql.org/pub/repos/apt/ xenial-pgdg main 11"
wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add -
apt-get update
apt-get -y install postgresql-11
sed -i.bak -re 's/^(host.*)ident/\1md5/' /etc/postgresql/11/main/pg_hba.conf
service postgresql start

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

useradd -mr omero
# Give a password to the omero user
# e.g. passwd 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. For the commands below to work, add if required the user you are currently logged in as to the newly created database:

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 step is run as root.

We recommend to create a virtual environment and install the Ice Python binding using pip:

# Create a virtual env and activate it
python3 -mvenv $VENV_SERVER

# Install the Ice Python binding
$VENV_SERVER/bin/pip install https://github.com/ome/zeroc-ice-py-ubuntu1604/releases/download/0.2.0/zeroc_ice-3.6.5-cp35-cp35m-linux_x86_64.whl

Install omero-py:

# Install omero-py
$VENV_SERVER/bin/pip install "omero-py>=5.6.dev4"

Download and unzip OMERO.server:

cd /opt/omero/server
SERVER=https://downloads.openmicroscopy.org/omero/5.6/server-ice36.zip
wget -q $SERVER -O OMERO.server-ice36.zip
unzip -q OMERO.server*

Change the ownership of the OMERO.server directory and create a symlink:

# change ownership of the folder
chown -R omero OMERO.server-*
ln -s OMERO.server-*/ OMERO.server

The following steps are run as the omero system user.

The variable OMERODIR set in settings.env above must point to the location where OMERO.server is installed. e.g. OMERODIR=/path_to_omero_server/OMERO.server.

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.

Configure the server:

omero config set omero.data.dir "$OMERO_DATA_DIR"
omero config set omero.db.name "$OMERO_DB_NAME"
omero config set omero.db.user "$OMERO_DB_USER"
omero config set omero.db.pass "$OMERO_DB_PASS"
omero db script -f $OMERODIR/db.sql --password "$OMERO_ROOT_PASS"
psql -h localhost -U "$OMERO_DB_USER" "$OMERO_DB_NAME" < $OMERODIR/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 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 $OMERODIR/etc $OMERODIR/var

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