Cytoscape WikiHow to set up Eclipse to develop Cytoscape plugins (draft)
Márcio Rosa da Silva
June 2005
Introduction
After some time trying to do this, I think I got [http://www.eclipse.org Eclipse] to work for me (instead of against me 
) so I think I should share this experience with others.
This document assumes that you have [http://www.eclipse.org Eclipse] installed and running.
Creating the project
Go to File->New->Project... then select Java Project.
On the next dialog, put a name for your project and click Finish.
[http://csresources.sourceforge.net/images/eclipse1.png]
Right click the new created project in the Package Explorer and select Properties
Then select Java Build Path on the left panel and Libraries in the
tabs on the right panel, then choose Add External JARs...
Add cytoscape.jar from the main Cytoscape folder and all the .jar
files from the lib/ folder inside the main Cytoscape folder. (you need 2 steps to do this, one for cytoscape.jar and another for the other .jar's)
http://csresources.sourceforge.net/images/eclipse2.png
Apply your changes
Now, create your plugin! You can find some help at [http://cytoscape.org/developer.php this page] from [http://cytoscape.org Cytoscape] website.
Running the plugin
To Run your plugin, select Run->Run... in Eclipse and click New (at the bottom-left part of the dialog) to create the settings to run your plugin .
Put a Name for the Run Target and choose cytoscape.CyMain as the Main class.
On the next tab ((x)= Arguments) put the path to your Cytoscape's plugins
folder as program arguments (you can add other arguments here, like preload your network, node/edge atributes, expression data, etc. See the Cytoscape's [http://cytoscape.org/manual/Cytoscape2_1Manual.pdf manual] for more information on the available command line options.
- Now you can run your plugin!