In the last post, I mentioned that I was having trouble getting the Cytoscape source code to run in Eclipse because I was missing libraries. It turns out that the cytoscape.bookmarks library files are generated at runtime (this I learned from the cytoscape-discuss board). However, I was still unable to run the Cytoscape program on Eclipse. As a solution, I installed the Subclipse plugin for Eclipse which allows for subverision from within Eclipse. I created a Java Project from Subclipse, and installed Jakarta Ant (which is necessary to build Cytoscape, as mentioned in the README file that can be found in the repository), and I managed to get the source code up and running! :)

By the end of last week and Monday of this week, I started focusing on learning more about Ant. I’ve been reading:

Java Development with Ant – By Erik Hatcher and Steve Loughran

Ant – The Definitive Guide – By Steve Holzner

It turns out that Ant isn’t that hard to pick up if you know XML and Java (and Make for C and C++ projects).

Today, and for the next few days, I have and will continue to try to debug a simple plugin in Eclipse. I’ve followed the “Setting Up Eclipse For Plugin Development” tutorial, but I still have a few issues that I will have to work out before I can say I can entirely debug plugins in Eclipse.

By the way, I’ve added a “Progress” page to this blog to make tracking the progress of this project easier.