Launch and Debug your App using Eclipse


This page describes:

Launching Cytoscape from inside Eclipse



Cytoscape should launch and you should see the console output in the Console View.


Any time you want to launch Cytoscape click on the External Tools toolbar button.

Debugging your App

Any time you want to debug your app you need to do two things:

  1. Lauch Cytoscape in debug mode.
  2. Connect to the Cytoscape process from the Eclipse debugger.

Launching Cytoscape in Debug mode

To start Cytoscape in debug mode from the console, run Cytoscape with debug as the first command line argument:

To start Cytoscape in debug mode from inside Eclipse create another external tool launch configuration like the one created above.


The message Listening for transport dt_socket at address: 12345 will appear in the console. The Cytoscape process is blocked waiting for a connection from an external debugger.

Connecting to Cytoscape with the Eclipse Debugger



The Eclipse Debugger

Here is a nice tutorial on how to use the Eclipse debugger:

The Eclipse Java debugger supports a very nice feature called Hotswap. The debugger allows you to make changes to your code, compile them and run them without leaving the debugger or needing to restart Cytoscape. Simply edit some code and save the file and the new code should replace the old code in the debug session. Keep in mind that this only works with edits that do not change top level declarations. For example if you add a parameter to a public method or add a field to a class then the debugger will inform you that it cannot replace the old code. When this happens you will have start a new debug session.


It is important to disconnect the debugging process when finishing executing Cytoscape. This will happen naturally when the program exits gracefully, but during the debug process, it is common to terminate execution without going through the proper quit procedure. As a result, this can leave an orphaned process listening on port 12345. The next time you try to execute you’ll see an error at start up as you attempt to open a second connection on the same port.

ERROR: transport error 202: bind failed: Address already in use
ERROR: JDWP Transport dt_socket failed to initialize, TRANSPORT_INIT(510)
JDWP exit error AGENT_ERROR_TRANSPORT_INIT(197): No transports initialized [debugInit.c:750]
FATAL ERROR in native method: JDWP No transports initialized, jvmtiError=AGENT_ERROR_TRANSPORT_INIT(197)
/Applications/Cytoscape_v3.5.0-RC2/ line 80:  3052 Abort trap: 6           $script_path/framework/bin/karaf "$@"

For Mac / Linux / Unix users:

If you encounter this error, you can query the list of open files (lsof) that are listening to a our debug TCP port with this command from a terminal:

     lsof -t -i :12345

To quickly find and kill the process that is causing the problem, you can run:

     kill -9 $(lsof -t -i :12345)   

For Windows users:

     netstat -aon | findstr :12345   

     taskkill /F /PID XXX      (where XXX is replaced by the process id)

Cytoscape_3/AppDeveloper/Cytoscape_App_Ladder/Launch_And_Debug_From_Eclipse (last edited 2017-04-26 19:52:39 by AdamTreister2)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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