This guide is designed for an installation on Ubuntu 16.04+ (18.04 tested).
This guide works for Cytomine-bootstrap, Cytomine-Core and Cytomine-IMS development versions released from January 2019.
If you are interested to develop new modules for Cytomine-Core (e.g. new web services, new entity in the data model,...) and/or new modules for Cytomine-IMS (e.g. support of a new image format, new image web service, ...), follow this guide. Note that if you are only interested to plug a new script of image analysis algorithm, we recommend instead to look at the [DOC] Interoperability (data & algorithms) documentation page.
This guide will help you to install Cytomine on your local machine for development. First, we will make a regular installation of Cytomine, then tweak it to allow you to develop and test on your own computer.
Step 1 - Make a regular installation of Cytomine
Follow the guide Install Cytomine on Linux to make a regular installation of Cytomine.
In particular, install Docker (step 1), retrieve Cytomine bootstrap (step 2) and configure your instance (step 3).
In the configuration (
- the parameter
CORE_DEVELOPMENTto true if you want to develop on Cytomine-core.
- the parameter
IMS_DEVELOPMENTto true if you want to develop on Cytomine-IMS.
Development on Core and IMS can be enabled together.
Then, initialize your instance deployment (step 4) and deploy your instance (step 5).
Step 2 - Install development requirements
Cytomine-Core and Cytomine-IMS mainly rely on Java, Groovy and the Grails framework.
Oracle Java 8
Check Java version with
java -version. The output should be something like '
java version "1.8.0_191"'.
Grails & Groovy with sdkman
Fix Grails installation for Java 8
Restart a terminal in order the environment variable
$GRAILS_HOME is effective. Fix Grails 2.4.4 to work with Java 8:
It may be also useful to install a modern web browser such as Google Chrome, to navigate into the web interface.
Step 3 - Install an integrated development environment
We recommend to use Intellij IDEA Ultimate Edition. The following instructions considers it is the case. A free license of the application can be obtained with an academical email address.
Install Intellij IDEA
Download Intellij IDEA Ultimate Edition on their website: https://www.jetbrains.com/idea/download/#section=linux
Install it by following the instructions on their website: https://www.jetbrains.com/help/idea/install-and-set-up-intellij-idea.html
Create Cytomine-core project in Intellij IDEA
This tutorial presents the configuration of Cytomine-core project in Intellij IDEA. For Cytomine-IMS, read the supplementary required steps at the end of this document.
Click on Check out from version control and choose Git in the contextual menu. The repository URL for Cytomine-core is
You can also manually clone the repsoitory with
git clone and open the project in Intellij in File > Open.
Configure Java SDK
Go to File > Project Structure > Project to choose the project SDK corresponding to the previously installed version of Java.
If the previously installed Java JDK is not available in the dropdown list, click on New and reference the SDK with the path
Configure Grails SDK
Go to Tools > Grails > Configure Grails SDK. You can retrieve the Grails SDK Home by running the command
Then, click on Ok.
If Grails is not available in the Tools menu, first go on the Project panel on left, right click on the project name "Cytomine-Core" then choose Add framework support and choose Grails.
If the source root of the project is not detected, in the Project panel on left, right click on
grails-app folder and then Mark Directory as > Source root.
Install Grails plugins
We will now install required Grails plugins. Go to Tools > Grails > Run Grails Command (Shortcut: Ctrl + Alt + G) and enter
clean-all as command.
Run a new Grails Command:
compile. It will download required plugins, install and compile them.
Do not pay attention to potential warnings related to
Edit running configuration
Go to Run > Edit Configurations.
First, delete the configuration named "Grails: Cytomine" by clicking on the Minus button on top-left or with Alt+Delete.
Click on the + button on top-left corner, and create a new configuration by selecting "Grails" in the list. Fill the form with
- Cytomine as application,
for the command line:
for the VM options:
Then click on Ok.
Link bootstrap configuration with development environment
The last operation before running Cytomine-core is to link the configuration established in the bootstrap (see Step 1) with the Cytomine-core development environment. As the core is no more running in a Docker container, we need to make this link manually.
In your Cytomine-Core project, open the
Cytomine-core/grails-app/conf/Config.groovy file. In the first lines, update the
grails.config.locations property in the development environment with the path to the generated core configuration (
configs/core/cytomineconfig.groovy) in your bootstrap (see Step 1). For example, at line 9,
Step 4 - Run Cytomine locally and develop
Make sure that Cytomine bootstrap is deployed (
restart.sh has finished) and run the run configuration we created before in Intellij. You can now access the core development server at http://CORE_URL:8080 (where
CORE_URL is given in bootstrap
configuration.sh) to test your core development environment. It will rely on other containers installed by Docker but use your own core development environment.
If you update your bootstrap configuration, run the following command to generate new configuration files and redeploy the containers.
Then run Cytomine-core in Intellij.
If you set
IMS_DEVELOPMENT to true in step 1, to run Cytomine-IMS locally, you need to create a new project in Intellij by cloning
and perform the supplementary steps detailed below before to run the configuration in Intellij.
Supplementary steps to run IMS locally
Install locally the IMS required libraries
If you want develop on IMS, the IMS will run on your machine and you will need all the dependencies of IMS.
Update your /etc/hosts
If you kept the default configuration in the bootstrap (step 1), append to your
Fix Background plugin
If you still develop with a version that use Background plugin, in order to avoid the
org.codehaus.groovy.grails.commons.ConfigurationHolder: class not found error when compiling Cytomine-IMS, edit the file
~/.grails/2.4.4/projects/IMS/plugins/background-thread-1.6/BackgroundThreadGrailsPlugin.groovy, by replacing
Use an available port
If you run Core and IMS locally at the same time, each component has to run on a dedicated port. In this guide, the port 8080 is used for Cytomine-core. For Cytomine-IMS you can use the port 9080 for example. Go to Run > Edit Configuration and update the port on which IMS will run :
Link bootstrap configuration with development environment
In your Cytomine-IMS project, in the
Cytomine-IMS/grails-app/conf/Config.groovy file of your Cytomine-IMS project,
Supplementary steps to run new VueJS front-end locally
We have started to migrate our front-end into a brand new VueJS front-end. For now, it has not been integrated into Cytomine-core (still running in Grails 2.4) and will be done in the future when the whole application will be migrated to Grails 3.
To run the new front-end, first deploy the application with Cytomine-core listening on
localhost-core:8080. Then, simply run
to run a development server. It will launch a server on
localhost:8085 which will act as a proxy to
localhost-core:8080 so that the VueJS front-end will override the old one on
To make the changes persistent, run
and copy the produced bundle in
Cytomine-core/web-app/application/views/v2.0/dist directory of the Cytomine-core project.
If you encounter a "
java.lang.OutOfMememoryError: PermGen space" error, add the option
-XX:+CMSClassUnloadingEnabledto the JVM, when running Cytomine-Core. In Intellij, go to Run > Edit Configurations and add it in the VM options field.
As nginx will try to contact your machine, you may need to allow docker containers to contact port 8080 & 9080. Here is the command with UFW