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Installing the new software architecture will make all your previously installed software impossible to execute. However, all data produced by jobs in of course kept.

1) Make backups

Check [HOWTO] Backup & restore data with Docker to backup your databases.

2) Get the last release of Cytomine-bootstrap from ULiege

sudo apt-get install git
git clone
cd Cytomine-bootstrap

3) Fix new paths where software code will be stored.

You need to create yourself these directories (mkdir -p) and make sure that Cytomine has rights to read/write in it before running installation.

For example:


4) Install latest release by running

cd Cytomine-bootstrap
sudo sh

The new software-router is launched. 

A new container named "slurm" acts as a local processing server. It is automatically added to Cytomine. If the SERVER_SSHKEYS_PATH directory is empty, it will automatically create a SSH keys pair for Cytomine.

5) Add trusted software repositories to get software on your instances.

Follow the instructions in [HOWTO] Manage software and servers for administrators in the section Manage software user repositories.

Software from this trusted repository are added to Cytomine.

You can check that everything works by checking software-router logs

sudo docker logs software_router
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