How to set up Eclipse to develop Cytoscape plugins (draft)
Márcio Rosa da Silva
After some time trying to do this, I think I got Eclipse to work for me
(instead of against me :-) ) so I think I should share this experience with
This document assumes that you have Eclipse installed and running.
Creating the project
- Go to
File->New->Project... then select
- On the next dialog, put a name for your project and click
- Right click the new created project in the
Package Explorer and select
- Then select
Java Build Path on the left panel and
Libraries in the
tabs on the right panel, then choose
Add External JARs...
cytoscape.jar from the main Cytoscape folder and all the
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)
Apply your changes
- Now, create your plugin! You can find some help at this page from 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
- 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
manual for more
information on the available command line options.
- Now you can run your plugin!
Note: Before running the plugin for the first time, you may need to put a .jar of the plugin in some place Cytoscape will search for plugins (e.g. the plugins/ folder inside the Cytoscape installarion folder). Otherwise, Cytoscape will not find your plugin. You don't need to generate the .jar for every run, only the first time. Cytoscape only needs to know your plugin is there, but the actual code will be run from the files in your Eclipse project.