Question

Let me begin by saying I am not an extremely experienced programmer and would would greatly appreciate it if you could fully specify any steps you might otherwise skip mentioning.

I am currently in the initial stages of plugin development for Cytoscape, I have created a java project in Eclipse and done the following

1. I have added cytoscape.jar as an external library

2. I have added “-p C:\Program Files\Cytoscape_v2.8.1\plugins” in the arguments tab under “Program Arguments”

When I try running the plugin it loads cytoscape but without any installed plugins (0 plugins in plugin manager) furthermore it also has curtailed menu options (cannot import certain files, the options just aren’t there anymore)

I suspect it is because I need to include more jar files as external libraries, however I am not sure which ones.

I am using Eclipse Indigo and Cytoscape 2.8.1.

I don’t think it is a problem with the plugin code since I have used the source code from an existing plugin as a test plugin.

Thanks for your patience and time.

Sudipto

PS: I have already looked at the following without much success
http://cytoscape.wodaklab.org/wiki/SettingUpEclipseForPluginDevelopment

Answer 1

Figured out the issue, didn’t notice the space in my plugin path, quotes solved the whole issue.

Also, you have to set both the location of a jar file of YOUR project and the plugins. This may not be very clear with eclipse, because the directions for eclipse are slightly different from those for netbeans.

So if you export your jar to /workspace, and you have cytoscape in /Applications/Cytoscape_v2.8.3 (OS X), then put the following in the run configuration as two separate lines:

-p "/Applications/Cytoscape_v2.8.3/plugins" 
-p "/workspace/jar_file_export_folder"