Bioinformatics Institute


  Frequently Asked Questions

  1. What do I need to download to build and run workflows by dragging and dropping?
    You will need to download Wildfire and GEL. Wildfire is the program that you use to draw your workflows. GEL is needed to run these workflows.
  2. I downloaded Wildfire 2.0 Windows Installer, and when I run it, I get the error "To help protect your computer, Windows has closed this program". What's wrong? The error message is caused by a featured called Data Execution Protection (DEP) which is enabled by default in Windows XP SP2. You must change the settings to allow Windows to execute the Wildfire 2.0 Windows Installer. More information can be found on Microsoft's website in the article How to Configure Memory Protection in Windows XP SP2.
  3. Do I need a Unix machine?
    GEL only runs on Unix-style machines, so yes, you will need a Unix machine (Linux will do) to run your workflows.
  4. Do I really have to use Unix?
    Not really. Wildfire can run on a normal Windows PC and send the workflows for processing on a Unix machine. If someone can set up GEL on a Unix machine for you, you don't need to use Unix much.
  5. I installed Wildfire in Windows but when I try to run it, I get the error "'java' is not recognized as an internal or external command, operable program or batch file". What is wrong here?
    There is likely something wrong with your windows configuration. Try installing Sun's JRE.
  6. Do I need administrator privileges to install and run Wildfire or GEL?
    No. Wildfire and GEL can both be installed without administrator privileges. They can be installed in your home directory.
  7. Do I need to set up any special services to use Wildfire and GEL in client/server mode?
    In most cases, no. Wildfire/GEL in client/server mode only requires an ssh connection. Most modern Unix and Linux configurations allow for ssh connections.
  8. I am a command-line expert and don't like programming using drag and drop. Do I have to use Wildfire to run workflows?
    No you don't. You can write GEL scripts "by hand" using your favourite editor, and then execute them by running the GEL interpetor on the command-line.
  9. Can I submit the GEL interpetor to the cluster queue as well?
    Yes. If you run the interpretor through the cluster's queue using PBS, LSF or SGE, and if the compute nodes have been configured as submit nodes, it will run correctly.
    However, we have experienced one case where a cluster only had 8 cpu slots, and the scheduler managed to run 8 separate GEL interpretors concurrently. Thus the cluster ended up in a state of deadlock because the scheduler couldn't run any of the jobs submitted by these GEL interpretors, and these GEL interpetors would not terminate (and hence free up cpu slots to run the jobs) because their jobs weren't running.
  If your question isn't answered here, then you can email