Running and Developing Cytoscape 3 on Eclipse

Introduction

This is a tutorial document to learn how to run and develop Cytoscape 3 on Eclipse's OSGi Runtime (Equinox)

Requirments

• Java SE 5/6
• Eclipse 3.4
• m2eclipse

Procedure

Setting Up Your Environment

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

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 Integration

1. Start Eclipse.

2. Checkout Cytoscape 3 from the current SVN trunk: http://chianti.ucsd.edu/svn/cytoscape3/trunk/

3. Quit Eclipse

4. From command line, run mvn pax:eclipse. This command generates eclipse project files.

5. Start Eclipse again