GenePattern 3.9.0 Release Notes

Released October 1, 2014

GenePattern 3.9.0 requires Java 7 and contains several new features and fixes.

Also see:

New User Features

Disk Usage Quota

We have added a configurable disk usage quota for user files uploaded to the Files Tab. The default configuration disables quotas. 

  • A disk usage indicator is now visible on the far right hand side of the menu bar (1).
    • If disk quotas are disabled, the usage indicator will display the user's current disk usage.
    • If disk quotas are enabled, the usage indicator will display both the user's current disk usage and quota. The usage indicator will be yellow if disk usage is between 75% and 90% of the disk quota, and red if disk usage is greater than 90%.  
  • We have also added a Disk Quota page to the collection of Administration Server Settings pages (2). This page displays the Disk Usage and Disk Quota for all registered users.


Job Queue Status Indicator

The Job status page now provides more detailed information about the state of your job in our queue. If a job is pending, i.e. queued and not running, the Job Status page will now display a congestion status indicator for the queue. Green indicates a flowing queue, yellow a slightly congested queue, and red a highly congested  queue.

Job Status Details

The Job Status page now supports the optional display of a job's event history and usage statistics.  These can be accessed via the Show details link below the basic job information.

  • The event log includes the time a job was submitted to GenePattern, was submitted to the job queue, started running, finished running, and completed in GenePattern.  
  • The usage statistics include CPU usage, maximum memory, maximum swap space, maximum number of processes, and maximum number of threads.


Files Tab Directory Download

The files in a Files Tab directory can now be saved to the your local computer as a zip file.

New Internal Features

  • Record disk usage of job result files into the database.
  • Improved Job Runner logging. Record job resource usage status such as CPU time and total memory into the database.
  • Implement virtual job queue feature, needed for the Broad Institute hosted server.
  • Added job event log to the REST API.

Bug Fixes and Enhancements

  • Installer update addresses problems with installing GenePattern on Mavericks and update to Java 7. (not available in beta)
  • Corrected a problem with large file uploads to the job input form. The problem was an unintended timeout causing file uploads to fail after 5 minutes.
  • Corrected a problem (introduced in GP 3.8.2) with the launching of visualizers in pipelines.
  • Corrected a problem (introduced in GP 3.8.2) that caused pipelines to fail on the Broad Institute hosted GenePattern server after a server restart.
  • Corrected a problem (introduced in GP 3.8.2) with the REST API giving an incorrect empty list of job result files for a completed job.
  • Corrected a problem (introduced in GP 3.7) that allowed parallel steps in a pipeline to continue running on the job queue after a user canceled the pipeline.