GenePattern 3.9.5 Release Notes

Released September 25, 2015

GenePattern 3.9.5 requires Java 7+.

System requirements and known issues are detailed on the following pages. 

New User Features

  • It is now possible to submit a batch job, batching over text, numeric or dropdown parameters. See our batch guide for more details.​
    • Batch jobs can now be previewed by clicking the "Preview Batch" button



  • It is now possible to select multiple values in a text parameter or a dropdown parameter in supported modules.


  • Modules with numeric parameters that have a valid range will now enforce that range on the job input form. In the picture below, the maximum value that can be provided is 5 and the minimum is 0.


  • The software quality of pipelines can now be set from the pipeline designer.


  • When reloading a job with advanced parameters, the relevant advanced parameter sections will now automatically expand to display their values.

Bug Fixes and Enhancements

  • The option to launch a JavaScript viewer module in a new window is now more prominently displayed, having been moved to the top of the parameter listings.
  • GenePattern will now, by default, display the latest non-development version of a module, basing this assessment on the Software Quality attribute in the module's manifest.
  • Informational text has been added to the "Add Path or URL" dialog, explaining how to select multiple values.
  • File menus will now properly display when the left-hand panel is collapsed.

Admin Support

  • Java 8 is now officially supported.
  • When creating a module, it is now possible to specify how many values can be entered into text and drop-down parameters and also specify a valid range for numeric parameters.
  • Modules with a quality value of development or preproduction will now display a "This is a beta version of the module." message  on the Job Submit form.
  • A REST endpoint has been added to retrieve the system message. A similar endpoint has been added for those with administrative privileges to set the system message.
  • Improved support for different computational environments and programming languages.
  • An Amazon AMI for GenePattern 3.9.5 can be found at ami-45abe520.

Modules Released Since August 7, 2015

  • CLSFileCreator - A tool to create a class label (CLS) file. JavaScript version of this viewer is now available in beta.
  • ComparativeMarkerSelectionViewer - Views the results from ComparativeMarkerSelection. JavaScript version of this viewer is now available in beta.