omero BIBBOX application

This container can be installed as BIBBOX APP or standalone.

After the docker installation follow these instructions.

Standalone Installation

Clone the github repository. If necessary change the ports in the environment file .env and the volume mounts in docker-compose.yml.

git clone https://github.com/bibbox/app-omero
cd app-omero
docker network create bibbox-default-network
docker-compose up -d

The main App can be opened and set up at:

http://localhost:4080

Install within BIBBOX

Visit the BIBBOX page and find the App by its name in the store. Click on the symbol and select install. Then fill the parameters below and name your App, click install again.

Docker Images used

• postgres
• openmicroscopy/omero-server
• openmicroscopy/omero-web-standalone
• jupyter/omero-notebook

Install Environment Variables

• POSTGRES_PASSWORD = Password for Postgres DB (change in production environments)
• JUPYTER_TOKEN = Configures Jupyter Notebook to require the given plain-text token. Should be combined with USE_HTTPS on untrusted networks. Note that this option is not recommended for production!

The default values for the standalone installation are:

• POSTGRES_PASSWORD = changethispasswordinproductionenvironments
• JUPYTER_TOKEN = token

Mounted Volumes

postgres Container

• ./data/postgres:/var/lib/postgresql/data:rw

openmicroscopy/omero-server Container

• ./data/OMERO:/OMERO
• /home/simon/Documents/master_wsi_annot/LYTestCases/022:/OMERO/share

jupyter/omero-notebook Container

• ./data/notebooks:/home/jovyan/work
• /var/run/docker.sock:/var/run/docker.sock:rw