Launching cytoscape with a script

[Ruth Isserlin]

Hi, 

I am trying to launch cytoscape with the -S option with cytoscape 3.2.1.  If I have Cluego or wiki pathways apps installed it doesn't launch the script.  Is there a way to get around whatever those two apps are doing at startup so that I can run the script from the command line.  If I uninstall the two apps then the script works but I would rather not have to uninstall them every time I run a script.

Thanks, 

Ruth 

[Christian Lopes]

Hi,

ClueGO 2.5.1 fails to start in Cytoscape 3.2.1, and apparently that is preventing Cytoscape from being initialized properly when launched via a script with the -S option.

This is the logged error:

WARN  org.apache.felix.fileinstall - Error while starting bundle: file:/Users/christianlopes/CytoscapeConfiguration/3/apps/installed/cluego-plugin-2.1.5.jar

org.osgi.framework.BundleException: Unresolved constraint in bundle fr.upmc.ici.cluegoplugin.cluego-plugin [115]: Unable to resolve 115.0: missing requirement [115.0] osgi.wiring.package; (osgi.wiring.package=org.freehep.swing)

at org.apache.felix.framework.Felix.resolveBundleRevision(Felix.java:3974)

at org.apache.felix.framework.Felix.startBundle(Felix.java:2037)

at org.apache.felix.framework.BundleImpl.start(BundleImpl.java:955)

at org.apache.felix.fileinstall.internal.DirectoryWatcher.startBundle(DirectoryWatcher.java:1245)

at org.apache.felix.fileinstall.internal.DirectoryWatcher.startBundles(DirectoryWatcher.java:1217)

at org.apache.felix.fileinstall.internal.DirectoryWatcher.doProcess(DirectoryWatcher.java:509)

at org.apache.felix.fileinstall.internal.DirectoryWatcher.process(DirectoryWatcher.java:358)

at org.apache.felix.fileinstall.internal.DirectoryWatcher.run(DirectoryWatcher.java:310)

The good news is that the next version of Cytoscape (3.3) will prevent that from happening.

Also I cannot reproduce the issue on Cytoscape 3.2.1 with ClueGO 2.1.7.

Thanks,

Christian

[Barry Demchak]

Thanks, Christian ...

The v3.3 behavior would be because app startup exceptions are being caught and no longer obstruct startup??

Good news. I think Tim has also dealt with the ClueGo people on this point.

True, Tim???

Barry Demchak -- from my mobile phone

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[Tim Hull]

Yes - the App Manager changes should render this issue moot, as a failed app shouldn't cause AppsFinishedStartingEvent not to fire.