FlowJo v7.6.5 has a nifty command line feature extension for templates. (The FlowJo license allows Mac users to run both our C version (currently v9), and our Java version (currently v7.6.5); the feature sets of the 2 programs being slightly different).
For repetitive analysis workspaces amenable to templates, the command line feature allows one to use a script to run FlowJo, open a template, and have it load/analyze data, and output reports (layouts and tables). Nice to get your computer to do some work while you are at the ballgame, or home asleep!
Here is an example:
1. first set up your FlowJo template.
(note: currently Layouts and Tables work in templates, group FCS Export won't execute from templates)
2. On your mac use a text editor to write your shell script to open FlowJo with command line arguments.
-Below is a simple example shell script on my mac to open a FlowJo template, load some data (the template outputs a Table, and a Layout), then flowjo quits.
Screengrab before running the script:
(double click image to make larger)
One can use Mac OSX built in Applescript language and/or Automator to make more complex automation scripts, including Folder actions.