added logic to run python script for cytoscape on Mac
Fix the issue caused by Java 7u25. Basically, when Boss is started by web start, its appContext is null. This causes subsequent calls to fail and also UI update fails. The fix is to save the appContext of the main thread and pass it to the subsequent calls.

Also execute workflow components based on their workflow order. This is to facilitate the batch run of a workflow on multiple data sets.