Setting up an IDE : Command Line

Editor(s): PietMolenaar

Date: March 23, 2012

Status: First version


You need the following tools on your machine.



OS X 10.5 and later come with Maven pre-installed. However, Cytoscape 3.0 requires Maven 3.0 to build. To check which version your have, run this command:

mvn -version

If you don't have Maven installed, or your version is older than 3.0, follow these instructions:

  1. Download the binary distribution of Maven 3.0.
  2. Extract the archive to a convenient place.
  3. Include the Maven bin directory in your $PATH.

    1. Open ~/.bash_profile. If you don't have a .bash_profile, create one by entering:

      • touch ~/.bash_profile; chmod +x ~/.bash_profile

    2. Add a line like this:
      • export PATH="$PATH:/path/to/Maven/bin/"

    3. Save .bash_profile.

  4. Check to see if you installed Maven correctly by creating a new terminal window and entering the command:
    • which mvn

    • If the command prints nothing, then Maven was not installed correctly.



If your package manager doesn't have Maven, or if the Maven version it has is very old, follow the steps for installing Maven on the Mac.



Follow these steps.

Clone development environment from GitHub

First, you need to clone the Cytoscape 3 App Developer project:

git clone git:// app-developer


cd app-developer
mvn clean install

Run Application

Mac OS/Linux/Unix

cd target


cd target

Installing Apps

You can use the App Manager to install simple apps. For bundle apps, copy your JAR file to ~/CytoscapeConfiguration/3/apps/installed. If Cytoscape is already running, it will automatically attempt to load and start any bundles in that directory. If you overwrite a bundle there, Cytoscape will automatically restart that bundle and all of its dependents.


To enable remote debugging, pass the debug argument to the start up script:

Mac OS/Linux/UNIX

./ debug


cytoscape.bat debug

At this point, Cytoscape will pause until a debugger is connected to port 12345. For example, this is how you would start a debugging session using jdb:

jdb -attach 12345


List any issues, conflict, or dependencies raised by this proposal


How to Comment

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Cytoscape_3/AppDeveloper/SettingUpAnIDE/CommandLine (last edited 2013-04-09 21:03:16 by 192)

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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