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.
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.
To install Cytomine with the last features from ULiege research team, run these commands:
mkdir Cytomine/ cd Cytomine/ git clone https://github.com/Cytomine-ULiege/Cytomine-bootstrap.git cd Cytomine-bootstrap
configuration.sh file in your favorite text editor such as
Have a look at Cytomine configuration reference to configure your instance.
cd Cytomine-bootstrap nano configuration.sh
|To install Cytomine locally on your machine, you can keep the |
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.
127.0.0.1 localhost-core 127.0.0.1 localhost-ims 127.0.0.1 localhost-upload # if you enabled IRIS plugin 127.0.0.1 localhost-iris # if you enabled RETRIEVAL plugin 127.0.0.1 localhost-retrieval # if you enabled SOFTWARE plugin 127.0.0.1 rabbitmq
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
IMS_STORAGE_PATH=~/data/images IMS_BUFFER_PATH=~/data/_buffer FAST_DATA_PATH=~/data/images # if you enabled SOFTWARE plugin SOFTWARE_CODE_PATH=~/data/softwares/code SOFTWARE_DOCKER_IMAGES_PATH=~/data/softwares/images JOBS_PATH=~/data/jobs SERVER_SSHKEYS_PATH=~/data/ssh # if you enabled RETRIEVAL plugin RETRIEVAL_PATH=~/data/thumb # if you enabled BACKUP plugin BACKUP_PATH=~/data/backup
Don't forget to create all these directories (
mkdir) if they don't exist.
Generate your installation script with the command
sudo bash init.sh
Run the generated deployment script with the command
sudo bash start.sh # OR, in old versions: sudo bash start_deploy.sh
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.
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,
Password: retrieve it in
Cytomine-bootstrap/configs/core/cytomineconfig.groovy. Search the line with
grails.adminPassword. For example, in
'5366E276-7574-4155-84C1-E1EA5ECB1039', the password is 5366E276-7574-4155-84C1-E1EA5ECB1039
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.