Launching Cytoscape from Eclipse

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: https://github.com/cytoscape/cytoscape/wiki/Launch-and-Debug-from-Eclipse

Regular Launch Configuration

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

• Launch Cytoscape normally using the cytoscape.sh script.

  • git/cytoscape/cytoscape/gui-distribution/assembly/target/cytoscape/cytoscape.sh

• 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 cytoscape.sh 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”
• Browse to select the "model-impl_impl" Project (note: different from old screenshot)
• 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 (may be called "Dependencies" in newer versions of Eclipse)
• Click on “Bootstrap Entries” (or "Classpath Entries")
• Click on “Add External JARs…”

• Navigate to
  • git/cytoscape/cytoscape/gui-distribution/assembly/target/cytoscape/framework/lib/boot
  • Select all the jar files in this folder
• If using Java 11 or higher navigate to
  • git/cytoscape/cytoscape/gui-distribution/assembly/target/cytoscape/framework/lib/jdk9plus
  • Select all the jar files in this folder
• And like in the screenshot, also add JRE System Library to Bootstrap Entries (via Advanced...) and model-impl_impl to User Entries (via Add Projects...).
• 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. (This is the old case, with early Java 8.)
• Starting in v. 3.8 of Cytoscape, Java 11 is required. JavaFX 13 must be loaded separately.
• The Eclipse project has a project property specifying the Java version. If this doesn't agree with the version specified in the POM, confusing compiler errors will result.