Note

This documentation is for the new OMERO 5.3 version. See the latest OMERO 5.2.x version or the previous versions page to find documentation for the OMERO version you are using if you have not upgraded yet.

OMERO.web walkthrough installation Ubuntu 16.04 and IcePy 3.6

For convenience in this walkthrough the main OMERO.web 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_USER=omero
WEBPORT=80
WEBSERVER_NAME=localhost

Create local user omero, homedir /home/omero (run as root):

if [ -z "$(getent passwd omero)" ]; then

    useradd -m omero

fi

chmod a+X /home/omero

Install ZeroC IcePy 3.6. IcePy is managed by PyPI and will be installed as a part of OMERO.web requirements (run as root):

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

Install other dependencies (run as root):

apt-get update
apt-get -y install \
    python-pip


apt-get -y install \
    python-pillow \
    python-numpy


# install the latest version
pip install --upgrade pip
pip install --upgrade virtualenv

Install VirtualEnv - optional (run as root):

virtualenv /home/omero/omerowebvenv --system-site-packages

Install OMERO.web (run as omero):

curl -o OMERO.py.zip https://downloads.openmicroscopy.org/latest/omero5.3/py.zip

zip=$(ls OMERO.py*.zip)
zipname=${zip%.zip}
rm -f $zip
mv $(find . -name 'OMERO.py*' -type d) /home/omero/OMERO.py

Install VirtualEnv (run as root):

/home/omero/omerowebvenv/bin/pip install --upgrade -r /home/omero/OMERO.py/share/web/requirements-py27.txt

Configure OMERO.web and generate nginx template (run as omero):

source /home/omero/omerowebvenv/bin/activate

if [[ $WEBPREFIX = *[!\ ]* ]]; then
    /home/omero/OMERO.py/bin/omero config set omero.web.prefix "${WEBPREFIX}"
    /home/omero/OMERO.py/bin/omero config set omero.web.static_url "${WEBPREFIX}/static/"
fi

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

cat /home/omero/nginx.conf.tmp

Install NGINX (run as root):

#start-install
apt-get update
apt-get -y install nginx

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

service nginx start

Daemon (run as root):

cp ubuntu/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

ubuntu/run

omero-web-init.d example:

#!/bin/bash
#
# /etc/init.d/omero
# Subsystem file for "omero" server
#
### 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
#
### Redhat
# chkconfig: - 98 02
# description: Init script for OMERO.web
###

RETVAL=0
prog=omero-web

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


OMERO_PY=${OMERO_PY:-/home/omero/OMERO.py}
OMERO_USER=${OMERO_USER:-omero}
OMERO=${OMERO_PY}/bin/omero
VENVDIR=${VENVDIR:-/home/omero/omerowebvenv}

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

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

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

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