gistfile1.txt

[knishida@dhcp255-85]~% cytoscape-unix-3.2.0-SNAPSHOT/cytoscape.sh
             _                                    
   ___ _   _| |_  ___  ___  ___  __ _ _ __   ___  
  / __| | | | __|/ _ \/ __|/ __|/ _` | '_ \ / _ \ 
 | (__| |_| | |_| (_) \__ \ (__| (_| | |_) |  __/ 
  \___|\__, |\__|\___/|___/\___|\__,_| .__/ \___| 
       |___/                         |_|          

Cytoscape 3.2.0-SNAPSHOT

Hit '<tab>' for a list of available commands
   and '[cmd] --help' for help on a specific command.
Hit '<ctrl-d>' or 'osgi:shutdown' to shutdown Cytoscape.

Cytoscape 3.2.0-SNAPSHOT> cytoscape:script python /Users/knishida/hoge.py
Cytoscape 3.2.0-SNAPSHOT> java.lang.NullPointerException
	at org.cytoscape.scripting.internal.ExecuteScriptCommandTask.run(ExecuteScriptCommandTask.java:63)
	at org.cytoscape.work.internal.task.TaskRunner.run(TaskManagerImpl.java:262)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:439)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
	at java.util.concurrent.FutureTask.run(FutureTask.java:138)
	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:895)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:918)
	at java.lang.Thread.run(Thread.java:695)

I have this exact problem now. Do know what the cause is?

The problem is that you need to copy the jyphon jar file into the framework/../ext directory for anyone else (I think)