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 https://github.com/ome/zeroc-ice-debian10/releases/download/0.1.0/zeroc_ice-3.6.5-cp37-cp37m-linux_x86_64.whl

Install OMERO.web:

/opt/omero/web/venv3/bin/pip install "omero-web>=5.6.3"

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 properties below. Before changing the properties, run export PATH=/opt/omero/web/venv3/bin:$PATH:

• omero.web.wsgi_workers to (2 x NUM_CORES) + 1

  Note

  Do not scale the number of workers to the number of clients you expect to have. OMERO.web should only need 4-12 worker processes to handle many requests per second.

• omero.web.wsgi_args Additional arguments. For more details check Gunicorn Documentation.

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://127.0.0.1:6379/0"}}'
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:

#!/bin/bash
#
# /etc/init.d/omero-web
# Subsystem file for "omero" web
#
### BEGIN INIT INFO
# 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
### END INIT INFO
#
# chkconfig: - 98 02
# description: init file for OMERO.web
###

RETVAL=0
prog=omero-web

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

OMERO_USER=${OMERO_USER:-omero-web}
OMERO=/opt/omero/web/venv3/bin/omero
OMERODIR=/opt/omero/web/omero-web
VENVDIR=${VENVDIR:-/opt/omero/web/venv3}

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

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

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

case "$1" in
    start)
        start
        ;;
    stop)
        stop
        ;;
    restart)
        stop
        start
        ;;
    status)
        status
        ;;
    *)
        echo $"Usage: $0 {start|stop|restart|status}"
        RETVAL=1
esac
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

Maintenance

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

Please read OMERO.web maintenance.