GenePattern 3.9.1 Release Notes

Released January 16, 2015

GenePattern 3.9.1 requires Java 7 and contains several new features and fixes.

Users should see New User Features, which includes tags for jobs, and Bug Fixes and Enhancements.

Server administrators and developers see Admin Support.

Both users and administrators also refer to updates on the following pages.

New User Features

  • Users can now add comments and tags to jobs.
    • Add comments and tags when submitting a job (Screenshot above, step 1).
    • From the Job Status page, view, edit and add to comments and tags while a job is pending, running, or finished (Screenshots below, steps 2 & 3).
    • NOTE: Support for searching for jobs based on tags and comments will be available in a future release.

  • Users can select multiple files or input multiple URLs from the server file path dialog box (Screenshots below)
    • This function is enabled only when jobs are Batched (step 1)
    • Select Add Path or URL... button (step 2)
    • Add additional URL paths by pressing Add URL button to increase the number of input fields (step 3).
    • To select multiple files from the file system, Mac users press Command + click on the multiple files (step 4).
    • It is possible to submit batched jobs of mixed files from URLs and the file system.

  • Improved IGV launcher now works by sending files directly to a running IGV application on your machine.
  • Support for Javascript based visualizers
    • An application implemented in javascript can now be made into a GenePattern visualizer simply by adding the module category, JsViewer. 


Bug Fixes and Enhancements

  • Enable the use of a GenomeSpace directory as input to a GenePattern module.
    • E.g. for the CopyNumberInferencePipeline.
  • Add support for file by reference for file list parameters
    • E.g. when passing files to a module on GenePattern, URL links are given to the module and not the actual files to reduce file copying.

Admin support

We made a number of improvements to simplify the installation and administration of a GenePattern Server instance.

  • Enable use of MySQL database
  • Automatically generate database schema (run DDL scripts) when installing/updating the server
  • Improved directory layout to simplify server updates
  • Make it easy to customize the look and feel of the user interface (aka re-skin)
  • Enable configurable 'Contact Us' email address
  • Remove dependency on startup working directory, to make it easier to deploy GenePattern into an existing application server