Install Community Edition 2023.1

TIP

If you experiment any issue, please describe your problem precisely in our ticket system on Github. (opens new window)

WARNING

1. This version opens a new way to manage data within Cytomine. It is recommended for new projects starting from scratch, but not to upgrade projects already using any Cytomine Community Edition Legacy (version 2 or 3). Please contact us if you have such needs (opens new window).
2. Community Edition 2023.1 do not include any AI engine for the moment. This will be added in next release. So if you need to run AI within your Cytomine, please consider to install the last release of Cytomine Community Edition Legacy.

Install a Cytomine local instance

This installation procedure is for desktop or laptop computers running a Debian based Linux operating systems.

You must have installed Docker engine (opens new window) and git, and have root permissions (sudo in Debian/Ubuntu).

1. Clone the repository on your computer:

git clone --branch CE2023.1 https://github.com/Cytomine-ULiege/Cytomine-community-edition.git

2. Go into the cloned folder:

cd Cytomine-community-edition

3. Edit the file cytomine.template if you want to change default values (like URLs and/or SMTP setup)
4. Launch the Cytomine installer. This will create all the folders and files necessary to launch Cytomine with Compose:

sudo docker pull cytomine/installer
sudo docker run -v $(pwd):/install --user "$(id -u):$(id -g)" --rm -it cytomine/installer:latest deploy -s /install

5. Launch cytomine:

sudo docker compose up -d

⚠️ As a side effect, this last command will write in your local /etc/hosts file.

6. Use Cytomine : If you have kept the default values your Cytomine is now available on http://cytomine.local. By default, an admin account has been created for you. To connect to the platform in your browser, retrieve the randomly generated admin password by opening your cytomine.yml file and go to services: default: core : constant: ADMIN_PASSWORD:. You can use this password with the adminusername to get authenticated on your Cytomine. Once authenticated, update this admin password to a more personal one.

Install a Cytomine distant instance

This installation procedure is for servers running a Debian based Linux operating systems.

You must have installed Docker engine (opens new window) and git, and have root permissions (sudo in Debian/Ubuntu).

You also need to have set 3 URLs in your Domain Name Server. In this example it will be example.com, ims.example.com and upload.example.com.

1. Clone the repository on your server:

git clone https://github.com/Cytomine-ULiege/Cytomine-community-edition.git

2. Go into the cloned folder:

cd Cytomine-community-edition

3. Switch to the server instance deployment branch:

git switch ce-server-install

4. Edit the file cytomine.template if you want to change default values (like URLs and/or SMTP setup)
5. Edit the file configs/nginx/etc/nginx/nginx.conf.sample with the correct information if you want SSL encryption directly in your Cytomine
6. Launch the installer. This will create all the folders and files necessary to launch Cytomine with Compose:

sudo docker pull cytomine/installer
sudo docker run -v $(pwd):/install --user "$(id -u):$(id -g)" --rm -it cytomine/installer:latest deploy -s /install

7. Launch cytomine:

sudo docker compose up -d

8. Use Cytomine : You can now discover Cytomine by browsing the URL you chose for CORE URL. By default, an admin account has been created for you. To connect to the platform in your browser, retrieve the randomly generated admin password by opening your cytomine.yml file and go to services: default: core : constant: ADMIN_PASSWORD:. You can use this password with the adminusername to get authenticated on your Cytomine. Once authenticated, update this admin password to a more personal one. If you want to find this password using command line you can use :

cat cytomine.yml | grep ADMIN_PASSWORD:

Update configuration

If you want to change the configuration of a running instance :

1. Update your configuration in the cytomine.template file.
2. Relaunch the Cytomine installer to update your configuration file :

sudo docker pull cytomine/installer
sudo docker run -v $(pwd):/install --user "$(id -u):$(id -g)" --rm -it cytomine/installer:latest deploy -s /install

3. Restart your running instance :

sudo docker compose restart

Stop Cytomine

To stop your Cytomine instance, use :

sudo docker compose down

The server is stopped but data (databases and images) are preserved.