This guide requires Apple Mac OS Yosemite 10.10.3 or above.
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 Mac. In particular download Docker for Mac from Docker store and follows instructions. Docker for Mac requires Apple Mac OS Yosemite 10.10.3 or above.
Once Docker for Mac is running, Choose → Preferences from the menu bar and configure the runtime options described below.
On the Advanced tab, you can change resource limits available to Docker.
By default, Docker for Mac drastically limit the resources available to Docker. Cytomine requires more resources to run without issue.
CPUs: By default, Docker for Mac is set to use half the number of processors available on the host machine. Set the number of CPUs available to a number greater than 75% of the number of processors on the host machine.
Memory: By default, Docker for Mac is set to use
2 GB runtime memory, allocated from the total available memory on your Mac. Increase RAM to a number at least greater than 4GiB. It is highly recommended to set it to at least 75% of the total available memory on your Mac.
Swap: Configure swap file size as needed. The default is 1 GB. Set it to 3GiB.
Latest Cytomine ULiege release is available at: https://github.com/Cytomine-ULiege/Cytomine-bootstrap/releases/latest
Latest Cytomine ULiege release can be downloaded here: https://github.com/Cytomine-ULiege/Cytomine-bootstrap/releases/latest/download/Cytomine-bootstrap.zip
Download the archive and extract it.
wget https://github.com/Cytomine-ULiege/Cytomine-bootstrap/releases/latest/download/Cytomine-bootstrap.zip unzip Cytomine-bootstrap.zip
To install Cytomine ULiege latest developments, continuous builds or pre-releases, you can clone the Git repository:
git clone https://github.com/Cytomine-ULiege/Cytomine-bootstrap.git
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
XXX_URL variables unchanged. Be sure to use URLs that are not already used by other applications (avoid
localhost) to prevent conflicts.
Due to the isolated nature of Docker containers, some changes on your Mac network configuration are required to allow to communicate with Cytomine directly from your Mac (such as your browser).
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
Then, flush your Mac's DNS cache, so it doesn't get confused by any changes you've made to the hosts file.
sudo killall -HUP mDNSResponder
Data managed by Cytomine such as images are stored in directories mapped with your host machine. By default the
/Users directories (and thus sub-directories) can be mapped in the Docker engine. Check → Preferences from the menu bar and then File Sharing tab to change location.
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