Page tree
Skip to end of metadata
Go to start of metadata

This guide is designed for Linux Ubuntu 16.04+ (18.04 tested). Other distributions should be supported with slightly little modifications.

This page describes how to run a production-ready instance of Cytomine in a few steps, either on personal computers (such as laptops, desktops) or on larger servers. Once Cytomine's server is installed, your Cytomine instance can be accessed through a modern web browser or via clients using the RESTful API.

Step 1 - Install requirements

Cytomine runs in Docker containers, so that the only requirement is to install Docker.

Check official Docker documentation to install Docker for Ubuntu. In particular, choose Install using the repository, set up the repository and install Docker CE.

You can optionally improve your Docker installation with the post installation steps for Linux.

Step 2 - Retrieve Cytomine bootstrap

Download the archive and extract it.


To install Cytomine ULiege latest developments, continuous builds or pre-releases, you can clone the Git repository:

git clone

Step 3 - Configure your instance

Open file in your favorite text editor such as nano.

Have a look at Cytomine configuration reference to configure your instance.

cd Cytomine-bootstrap

Configure URLs

To install Cytomine locally on your machine, you can keep the XXX_URL variables unchanged.

Be sure to use URLs that are not already used by other applications (avoid localhost) to prevent conflicts.

Add the XXX_URL variable values into the /etc/hosts of your host machine.

sudo nano /etc/hosts

In the /etc/hosts, add the following lines and don't forget to adapt them with values you chose for XXX_URL variables.	localhost-core	localhost-ims	localhost-upload

# if you enabled IRIS plugin	localhost-iris 

# if you enabled RETRIEVAL plugin	localhost-retrieval

# if you enabled SOFTWARE plugin   rabbitmq

Configure data paths

All paths referenced in variables XXX_PATH must exist and be mappable in the Docker engine. To create the data in your $HOME, set paths with


# if you enabled SOFTWARE plugin

# if you enabled RETRIEVAL plugin

# if you enabled BACKUP plugin

Don't forget to create all these directories (mkdir) if they don't exist.

Step 4 - Initialize your deployment

Generate your installation script with the command

sudo bash

Step 5 - Deploy your instance

Run the generated deployment script with the command

sudo bash 
# OR, in old versions: sudo bash

Deployment can take some time, especially if it's the first time you install Cytomine on your host machine. All Docker container images have to be downloaded.

Step 6 - Check your running instance

When start up is finished, check the application is running in your browser on the URL specified in your CORE_URL variable (by default: localhost-core).

An admin account is created by default. To connect,

  • Username: admin
  • Password: retrieve it in Cytomine-bootstrap/configs/core/cytomineconfig.groovy. Search the line with grails.adminPasswordFor example, in grails.adminPassword='5366E276-7574-4155-84C1-E1EA5ECB1039', the password is 5366E276-7574-4155-84C1-E1EA5ECB1039

Once connected on http://localhost-core (if you kept CORE_URL = localhost-core), click on you name at the top right in the web interface, and go to Account to change the admin password.
  • No labels