Launching Cytoscape from Eclipse

Adam Treister edited this page Apr 26, 2018 · 14 revisions

How to Launch (and Debug, and Profile) Cytoscape from Eclipse

There are two ways to launch cytoscape from inside eclipse.

  • As an external tool
    • Easier to set up, more cumbersome to launch, slower to debug, some minor limitations, recommended for app developers
  • Directly using a regular launch configuration
    • Harder to set up, easier to launch, supports full-speed debug, supports YourKit profiler launch, recommended for core developers

External Tool Launch Configuration

Instructions are available on the App Dev Ladder:

Regular Launch Configuration

These instructions work on Mac and should work on Linux. Windows is probably similar.

  • Start by building Cytoscape from source.

  • Launch Cytoscape normally using the script. Or if you already have an external tool launch configuration use it to launch cytoscape.

    • git/cytoscape/cytoscape/gui-distribution/assembly/target/cytoscape/
  • Open a Terminal

  • Run this command

    • ps -A | grep java
    • Ubuntu Note: On Ubuntu, the ps command doesn't output the full command line arguments for a process, so I had to get the java process PID (in my case, 37012 ) and then do this: ps -fp 37012 -w > cytoscape_process.txt **
  • This will show the command that the script generates. We will create an eclipse launch config from this command.

    • If there is more than one java process Cytoscape is the one that ends with org.cytoscape.launcher.internal.Launcher
  • Go to eclipse, click the little down arrow next to the run button, and select Run Configurations…

    • This will open the Run Configuations Dialog
  • Click on “Java Application” and click the “New” button on the little toolbar above it.

  • Click on the Main tab (probably already open)
  • Give the run configuration a name such as “Cytoscape_HEAD”
  • In the “Main class” field enter the following:
    • org.cytoscape.launcher.internal.Launcher
  • Click on the Arguments tab
  • Go back to the terminal
  • Select all the VM arguments from the command (starting at -Xms2048M and up to but not including the -classpath argument)

  • Copy-paste the arguments into the “VM arguments” text area in the eclipse run configurations dialog.

  • Add the following argument to the VM arguments (very important!!!)
    • -Dkaraf.lock=false
  • Click on the Classpath tab
  • Click on “Bootstrap Entries”
  • Click on “Add External JARs…”

Note: these instructions changed for v3.7 with karaf update

  • Navigate to
    • git/cytoscape/cytoscape/gui-distribution/assembly/target/cytoscape/framework/lib/boot
  • Select the following jar files
    • branding-3.7.0-SNAPSHOT.jar
    • org.apache.karaf-launcher-3.7.0-SNAPSHOT.jar
    • org.apache.karaf-diagnostic-boot-4.2.0-SNAPSHOT.jar
    • org.apache.karaf-jass-boot-4.2.0-SNAPSHOT.jar
    • org.apache.karaf.main-4.2.0-SNAPSHOT.jar
    • org.osgi.core-6.0.0.jar
  • Click Apply
  • Click Run

To debug from Eclipse, you may need to add all of the Java Projects in the Source tab

You can now run/debug/profile Cytoscape directly from the eclipse toolbar. Enjoy :)

Known Issues

Some apps that rely on JavaFX may throw exceptions when attempting to load JavaFX classes.

  • I think this can be fixed by updating your Java install. Some earlier versions of Java 8 did not ship with the JavaFX classes.
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