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2013/03/20 Web Meetup

NBIC Galaxy at SURFsara's HPC cloud


March 20, 2013


10 am Central US Time (-5 GMT)


NBIC Galaxy at SURFsara's HPC cloud

Hailiang Leon Mei <hailiang DOT mei AT nbic DOT nl>
Galaxy Project Update



NBIC Galaxy (Andromeda) was migrated to a HPC cloud hosted by Surfsara in September 2012. This presentation discussed the setup of this HPC cloud and the architecture of our NBIC Galaxy, and shared our experience on the installation of the NBIC Galaxy using the Cloudman scripts. The presentation finished with a list of issues and our possible future plans.

The Galaxy Project Update focused on the new release process, and upcoming Data Manager features.

Call Technology

We will use the University of Iowa's Blackboard system for the call. Downloading and launching the required Java application takes a few minutes. Using a headphone with microphone to prevent audio feedback during the call is recommended.

Images/Logos/AppleLogo.jpg +Images/Logos/JavaLogo.png

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Images/Logos/AppleLogo.jpg + Images/Logos/JavaLogo.png + You

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If you are running any moderately recent version of OS X, you may need to take some additional steps.  See this RacoonLab posting for details.

How do I know I have this problem?

These two situations are known to be fixed with this solution:

  1. If the meeting.jnlp file downloads but doesn't launch automatically, or even after you double click on it then

    Start a shell, go to your downloads directory and type
    • javaws meeting.jnlp

    if you see 
    • Java Web Start splash screen process exiting .....

      Blackboard Hang
      Bad installation. No JRE found in configuration file
  2. Blackboard Collaborate launches, says loading, gets to 3 of 5 dots on the status indicator and then throws up a blank gray window


  • you probably have this problem.

How do I fix this problem?

In the shell enter

  • sudo /usr/libexec/PlistBuddy -c "Delete :JavaWebComponentVersionMinimum" \

You should then be able to launch the meeting.jnlp by double clicking on it.

You may also find that you receive a message indicating that the file cannot be opened because it was not downloaded from the Mac App Store. This can be worked around by right clicking the meeting.jnlp file and clicking "Open" in the menu that pops up. More details about this error can be found here.