Locked History Actions


2013/05/15 Web Meetup

Galaxy at Pathogen Portal


May 15, 2013



10 am Central US Time (-5 GMT)


Galaxy at Pathogen Portal

Andrew Warren, Virginia Bioinformatics Institute, Virginia Tech
Galaxy Project Update


Screencast, Slides 

Pathogen Portal Galaxy

Andrew Warren of the Cyberinfrastructure Division of the Virginia Bioinformatics Institute at Virginia Tech talked about their experience deploying Galaxy for Pathogen Portal, a highly customized Galaxy installation, and also about the group's objectives and future plans.

Dannon Baker brought the group up to speed on what's happening in the Galaxy project.

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

= Images/Icons/Frown.jpg

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

= Images/Icons/Smile.png

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.