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.
