Running and Developing Cytoscape 3 on Eclipse

Introduction

This is a tutorial document to learn how to run and develop Cytoscape 3 with Eclipse PDE.

Procedure

Setting Up Your Environment

To develop Cytoscape 3 on Eclipse, you need to install several software packages.

Eclipse

This tutorial is based on the latest version of Eclipse 3.4, called Ganymede. Several distributions are available on [http://www.eclipse.org/downloads/packages/ Eclipse web site]. You need to use one of the following:

• Eclipse Classic 3.4
• Eclipse for RCP/Plug-in Developers

Both of these distributions include PDE (Plugin Development Environment).

Subversion

Cytoscape 3 source code is managed by [http://subversion.tigris.org/ Subversion]. To access the repository, you need to install subversion client for Eclipse. In this tutorial, I'll use [http://subclipse.tigris.org/ Subclipse]. You can install the plugin from the eclipse's update manager. Do not forget to install SVNKit. Otherwise, you will get an error message when you try to check out repository ("Unable to load default SVN Client")

Repository locations are the following:

• Core Developers: svn+ssh://grenache.ucsd.edu/common/svn/cytoscape3

• Others: http://chianti.ucsd.edu/svn/cytoscape3/

You need to checkout the trunk directory.

Maven and Maven Integration for Eclipse

Cytoscape build system has been moved to Maven. To use maven on Eclipse, you need to follow [:MavenInfo:this] instruction.

Now your Eclipse is ready for Cytoscape 3 development!

Checkout and Create Cytoscape 3 Eclipse Project

In this section, you will learn how to create an Eclipse project from the fresh Cytoscape 3 checkout.

Checkout Cytoscape 3 Trunk

1. Start Eclipse

2. Checkout Cytoscape 3 from the current SVN trunk. Set project type to Java Project

3. Quit Eclipse

4. From terminal, run mvn clean install pax:eclipse. This command automatically generates Eclipse project files. This process takes about 10 minutes to complete.

5. Start Eclipse again

6. Select File → Import and import as Maven Project attachment:eclipse_core1.png

7. Select all pom files and press Finish