OMERO.web installation with OMERO.server on Debian 9 and IcePy 3.6¶
Please first read OMERO.server installation on Debian 9.
This is an example walkthrough for installing OMERO.web with OMERO.server using NGINX.
For convenience in this walkthrough, we will use the same configuration
options that are used for the installation of the OMERO.server and an additional option
specific to the OMERO.web installation. When following this walkthrough you can
either use your own values, or alternatively
source settings-web.env:
WEBPORT=80
export WEBPORT
Installing prerequisites¶
The following steps are run as root.
Install Pillow and Numpy:
apt-get -y install zlib1g-dev libjpeg-dev
apt-get -y install python-{pillow,numpy}
Install NGINX and Gunicorn:
apt-get -y install nginx gunicorn
Configuring OMERO.web¶
The following steps are run as root.
Install other OMERO.web dependencies using pip:
pip install -r OMERO.server/share/web/requirements-py27.txt
The following steps are run as the omero system user.
Configure and create the NGINX OMERO configuration file:
OMERO.server/bin/omero config set omero.web.application_server wsgi-tcp
OMERO.server/bin/omero web config nginx --http "$WEBPORT" > OMERO.server/nginx.conf.tmp
For more customization, please read Customizing your OMERO.web installation.
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:
mv /etc/nginx/sites-available/default /etc/nginx/sites-available/default.disabled
cp OMERO.server/nginx.conf.tmp /etc/nginx/conf.d/omero-web.conf
service nginx start
Installing OMERO.web apps¶
The following steps are run as the omero system user.
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 via pip to your OMERO.web virtual environment at any time.
Running OMERO.web¶
The following steps are run as the omero system user.
To start the OMERO.web client run:
OMERO.server/bin/omero web start
NGINX should already be running so you should be able to log in as the OMERO root user by going to http://localhost/ in your web browser.
In addition omero-web-init.d
is available should you wish to start OMERO.web automatically.
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 this script into the appropriate location:
cp omero-web-cron /etc/cron.daily/omero-web
chmod a+x /etc/cron.daily/omero-web
