GenePattern 3.2.3 Release Notes

Released June 1, 2010

New in this Release

Pipeline Execution Engine

GenePattern now has the capacity to run a larger number of pipelines concurrently. The release also addresses several known issues with pipelines, which include:

  • Providing graceful exit handling for existing jobs and pipelines when a server is shut down
  • Allowing pipelines to run when a GenePattern server uses an authenticating http proxy
  • Eliminating the deadlock that occurred when the number of running pipelines exceeded the number of threads available

LSF Integration

This release provides better integration between GenePattern and the LSF batch queuing system. Some of the improvements include:

  • Long-running LSF jobs continue to run when the GenePattern server restarts.
  • LSF jobs are removed from the queue when a user terminates or deletes the associated GenePattern job.
  • The GenePattern server can run many more concurrent LSF jobs because it now releases system resources that were previously held onto for the duration of each job.

This release also includes a plugin architecture to facilitate integration of other batch queuing systems into a GenePattern server. For more information on deploying LSF or implementing GenePattern on another batch queuing system, email

Other Fixes

  • GenePattern now recognizes user settings for Java visualizer flags.
  • Visualizers now work on client machines that require a proxy configuration.
  • GenePattern no longer relaunches deleted jobs flagged as PENDING upon server restart.
  • GenePattern now recognizes symbolic links to files on the server's file system when they are used as an input file to a module.
  • The installer will not install GenePattern in any directory with a space in the name except C:/Program Files/.

Known Issues

Known issues in GenePattern 3.2.3 include:

  • GenePattern does not support module names with spaces in them.
  • Some GenePattern modules do not work when the input filename contains a space character. Workaround: Rename the input file without a space character.
  • On Macintosh: Java Runtime Environment (JRE) 1.6.0_15 does not work. Workaround: The GenePattern team suggests updating to the most recent JRE (GenePattern 3.2.3 has been tested with 1.6.0_20)
  • On Windows 7:The StartGenePatternServer and StopGenePatternServer applications must be run as an administrator. To start or stop the GenePattern server, right-click on StartGenePatternServer.exe or StopGenePattnerServer.exe and select Run as administrator.
  • For GenePattern administrators who have changed the "input.file.mode" property (in the file) from default: GenePattern 3.2.3 only works with the default setting, input.file.mode=path.

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