Setting up an IDE : Eclipse

Editor(s): KeiichiroOno PietMolenaar

Date: July 5, 2012

Status: Updated for Eclipse Juno


This is an introduction to Cytoscape 3 App development for Eclipse users.


You need to know basics of Eclipse and Maven.

Install JDK

To develop Cytoscape 3, you need Java 6 or 7. If you find problems on Java 7, please let us know.

Setting up Eclipse

This procedure had been tested with latest version of Eclipse, Juno (4.2). You can use any version of Eclipse distribution, but we recommend to use Eclipse for RCP and RAP Developers or Eclipse IDE for Java Developers.

Use JDK, not JRE

Make sure eclipse is running in the JDK virtual machine; on Windows this is not default. To use JDK's VM, create a shortcut and edit the shortcut's property: eclipse.exe -vm "c:\your_path_to_JDK\bin\javaw.exe"

Installing Eclipse Plugins From Eclipse Marketplace

Eclipse Indigo and later include a feature called the Eclipse Marketplace. All of the following plugins are available from the Marketplace. To install an Eclipse plugin, open the Marketplace dialog (Help → Eclipse Marketplace), type the plugin name in the search box, and click Install.


Usually, you will be asked to restart Eclipse after installing plugins.

Eclipse Plugins to Install

You need to install some Eclipse plugins to develop Cytoscape 3 apps. All of the following are required to develop Cytoscape 3 (or any Java applications using Maven and Spring).


EGit provides Eclipse with Git integration. It is included with most Eclipse distributions, but in case yours doesn't, you'll need to install it to get the source code from our GitHub repositories.


M2Eclipse is an Eclipse plugin to integrate Maven. Now it is a part of Eclipse foundation, and it is a part of Eclipse distribution. You do not have to install this plugin in Juno.

Many useful documents are available from the project and we recommend to read them.

Checkout Cytoscape 3 App Developer's Template Project

  1. In the menu, select File → Import → Git → Projects from Git → URI.

  2. Under URI, paste Eclipse will fill in the other fields for you automatically:

    • git-settings.png

  3. Under Initial branch select:

    • master if you want to develop an app using the latest stable release of Cytoscape, or

    • develop if you want to develop an app using the latest Cytoscape sources in the repository.

  4. Click Next.

  5. Select Import as general project.

  6. Click Next.

  7. Click Finish.

  8. Now you should have a project in Eclipse called cytoscape-app-developer.

  9. Right click on the project and select Configure → Convert to Maven Project.

  10. You should end up with a project that looks like this:
    • plugin-template0.png

Build App Developer's Template Project

  1. Right-click cytoscape project top folder

  2. Select Run As → Maven Build

  3. Type clean install in the Goals text box

  4. Click Run button

Now you can see the following directory structure under target directory (if you cannot see target, press f5 to refresh your workspace):


Run Cytoscape 3

  1. Open command-line terminal.
  2. Go into target directory you've just created with m2eclipse plugin

  3. Execute (for unix/mac) or cytoscape.bat (windows)

If you can run Cytoscape, now you are ready to code your app.

Create the App

There are two types of apps for Cytoscape 3 and you can use Eclipse for both of them.

Simple App

  1. Select New → Java Project

  2. Enter project name. This can be anything. In this example, we use Cy3SimpleApp as a sample app name.

  3. Add cytoscape-app-api jar file as a library

  4. Right-click src folder and create a class file HelloWorldApp. Use org.cytoscape.sample as its package name

  5. Create Manifest file. It's just a text file named MANIFEST.MF. The only entry you need to write in this file is the following:

    • Manifest-Version: 1.0
      Cytoscape-App: org.cytoscape.sample.HelloWorldApp

      This is your App's main class name. Be sure to include a return at the end of the last line or it may be excluded upon export!

  6. Your project directory looks like this:
    • simple-plugin1.png

  7. Write App main class:
    •    1 package org.cytoscape.sample;
         3 import;
         4 import;
         6 public class HelloWorldApp extends AbstractCyApp {
         8         public HelloWorldApp(CyAppAdapter adapter) {
         9                 super(adapter);
        11                 System.out.println("Hello Cytoscape 3!");
        12         }
        13 }
  8. Select File>Export

  9. Select JAR FIle and click Next

  10. Uncheck MANIFEST.MF file. Otherwise, two manifest files will be created in the JAR!

    • export1.png

  11. Type app jar file name and click Next

  12. Leave all settings as-is and click Next

  13. Select Use existing manifest from workspace and specify the one you've just created

    • simple-plugin2.png

  14. Click Finish. Make sure the app jar file exists in the directory you specified above.

Test your app

  1. Run Cytoscape from command-line
  2. Select Apps>App Manager

  3. Select Import Local App tab

  4. Click Select button and select the app jar file you've created

  5. You can see Hello Cytoscape 3! in the console

For more realistic example, please try this tutorial:

Tutorial:Creating a Simple Cytoscape 3 App

Cytoscape 3 Bundle App

If you want to create Cytoscape 3 Native bundle app, please try the following tutorial:

Tutorial:Creating an OSGi Bundle Cytoscape 3 App


If you find problems or have questions, please let us know.

Cytoscape_3/AppDeveloper/SettingUpAnIDE/Eclipse (last edited 2013-03-25 21:05:51 by server2)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

MoinMoin Appliance - Powered by TurnKey Linux