OMERO.server installation on Ubuntu 14.04 and 16.04

This is an example walkthrough for installing OMERO on Ubuntu, using a dedicated system user, and should be read in conjunction with Setting up OMERO.web. 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.

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 the following file:

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

OMERO_WEB_PORT=80

export OMERO_DB_USER OMERO_DB_PASS OMERO_DB_NAME OMERO_ROOT_PASS OMERO_DATA_DIR OMERO_WEB_PORT

export PGPASSWORD="$OMERO_DB_PASS"

settings.env

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,pillow,numpy,scipy,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 on Ubuntu 14.04:

# install Postgres
apt-get -y install apt-transport-https
add-apt-repository -y "deb https://apt.postgresql.org/pub/repos/apt/ trusty-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

To install PostgreSQL 9.6 on Ubuntu 16.04:

# 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=http://downloads.openmicroscopy.org/latest/omero5.3/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

Installing and running OMERO.web

OMERO.web is deployed using Nginx, for more details on how to install and run the OMERO.web client see OMERO.web walkthrough installation Ubuntu 16.04 and IcePy 3.6.

The following steps are run as root.

To install the latest stable version of Nginx on Ubuntu 14.04, run the following commands:

# required to install more recent version of nginx
# without this, the version installed is 1.4.6
add-apt-repository -y ppa:nginx/stable

apt-get update
apt-get -y install nginx

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 an init.d script is available should you wish to start OMERO automatically.

omero-init.d

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/OMERO.server/etc ~omero/OMERO.server/var

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

Regular tasks

The following steps are run as root.

The default OMERO.web session handler uses temporary files to store sessions which should be deleted at regular intervals, for instance by creating a cron job:

OMERO_USER=omero
OMERO_SERVER=/home/omero/OMERO.server
su - ${OMERO_USER} -c "${OMERO_SERVER}/bin/omero web clearsessions"

Copy the following commands into the appropriate location:

cp omero-web-cron /etc/cron.daily/omero-web
chmod a+x /etc/cron.daily/omero-web

omero-web-cron