OMERO.web installation on Debian 10 and IcePy 3.6

Please first read OMERO.server installation on Debian 10.

This is an example walkthrough for installing OMERO.web in a virtual environment using a dedicated system user. Installing OMERO.web in a virtual environment is the preferred way. For convenience in this walkthrough, we will use the omero-web system user and define the main OMERO.web configuration options as environment variables. Since 5.6, a new OMERODIR variable is used, you should first unset OMERO_HOME (if set) before beginning the installation process.

The following steps are run as root.

If required, first create a local system user omero-web and create directory:

useradd -m omero-web

mkdir -p /opt/omero/web/omero-web/etc/grid
chown -R omero-web /opt/omero/web/omero-web

Installing prerequisites

The following steps are run as root.

Install dependencies:

apt-get update

apt-get -y install unzip

apt-get -y install python3
apt-get -y install python3-venv

apt-get -y install nginx

Optional: if you wish to use the Redis cache, install Redis:

apt-get -y install redis-server

service redis-server start

Creating a virtual environment

The following steps are run as root.

Create the virtual environment. This is the recommended way to install OMERO.web:

python3 -mvenv /opt/omero/web/venv3

Install ZeroC IcePy 3.6:

/opt/omero/web/venv3/bin/pip install --upgrade

Install OMERO.web:

/opt/omero/web/venv3/bin/pip install "omero-web>=5.6.1"

Installing OMERO.web apps

A number of apps are available to add functionality to OMERO.web, such as OMERO.figure and OMERO.iviewer. See the main website for a list of released apps. These apps are optional and can be installed, as the root user, via pip to your OMERO.web virtual environment and configured as the omero-web system user, at any time.

Configuring OMERO.web

The following steps are run as the omero-web system user.

For convenience the main OMERO.web configuration options have been defined as environment variables. You can either use your own values, or alternatively use the following ones:

export WEBSESSION=True
export OMERODIR=/opt/omero/web/omero-web
export WEBPORT=80
export WEBSERVER_NAME=localhost

Configure OMERO.web and create the NGINX OMERO configuration file:

export PATH=/opt/omero/web/venv3/bin:$PATH

omero config set omero.web.application_server wsgi-tcp
omero web config nginx --http "${WEBPORT}" --servername "${WEBSERVER_NAME}" > /opt/omero/web/omero-web/nginx.conf.tmp

For more customization, please read Customizing your OMERO.web installation.

Configuring Gunicorn

The following steps are run as the omero-web system user.

Additional settings can be configured by changing the following properties:

Configuring NGINX

The following steps are run as root.

Copy the generated configuration file into the NGINX configuration directory, disable the default configuration and start NGINX:

sed -i.bak -re 's/( default_server.*)/; #\1/' /etc/nginx/nginx.conf
rm /etc/nginx/sites-enabled/default
cp /opt/omero/web/omero-web/nginx.conf.tmp /etc/nginx/conf.d/omeroweb.conf

service nginx start

Running OMERO.web

The following steps are run as root.

Install WhiteNoise:

/opt/omero/web/venv3/bin/pip install --upgrade 'whitenoise<4'

Optional: Install Django Redis:

/opt/omero/web/venv3/bin/pip install 'django-redis<4.9'

The following steps are run as the omero-web system user.

Optional: Configure the cache:

omero config set omero.web.caches '{"default": {"BACKEND": "django_redis.cache.RedisCache","LOCATION": "redis://"}}'
omero config set omero.web.session_engine 'django.contrib.sessions.backends.cache'

Configure WhiteNoise and start OMERO.web manually to test the installation:

omero config append -- omero.web.middleware '{"index": 0, "class": "whitenoise.middleware.WhiteNoiseMiddleware"}'

omero web start

# Test installation e.g. curl -sL localhost:4080

omero web stop

Automatically running OMERO.web

The following steps are run as root.

Should you wish to run OMERO.web automatically, a init.d file could be created. See below an example file omero-web-init.d:

# /etc/init.d/omero-web
# Subsystem file for "omero" web
# Provides:             omero-web
# Required-Start:       $local_fs $remote_fs $network $time omero postgresql
# Required-Stop:        $local_fs $remote_fs $network $time omero postgresql
# Default-Start:        2 3 4 5
# Default-Stop:         0 1 6
# Short-Description:    OMERO.web
# chkconfig: - 98 02
# description: init file for OMERO.web


# Read configuration variable file if it is present
[ -r /etc/default/$prog ] && . /etc/default/$prog


start() {
    echo -n $"Starting $prog:"
    su - ${OMERO_USER} -c ". ${VENVDIR}/bin/activate;OMERODIR=${OMERODIR} ${OMERO} web start" &> /dev/null && echo -n ' OMERO.web'
    sleep 5
    [ "$RETVAL" = 0 ]

stop() {
    echo -n $"Stopping $prog:"
    su - ${OMERO_USER} -c ". ${VENVDIR}/bin/activate;OMERODIR=${OMERODIR} ${OMERO} web stop" &> /dev/null && echo -n ' OMERO.web'
    [ "$RETVAL" = 0 ]

status() {
    echo -n $"Status $prog:"
    su - ${OMERO_USER} -c ". ${VENVDIR}/bin/activate;OMERODIR=${OMERODIR} ${OMERO} web status"

case "$1" in
        echo $"Usage: $0 {start|stop|restart|status}"
exit $RETVAL

Copy the init.d file, then configure the service:

cp omero-web-init.d /etc/init.d/omero-web
chmod a+x /etc/init.d/omero-web

update-rc.d -f omero-web remove
update-rc.d -f omero-web defaults 98 02

Start up services:

service redis-server start

service nginx start
service omero-web restart


The following steps are run as the omero-web system user.

Please read OMERO.web maintenance.