GenePattern 3.2.4 Release Notes

Released January 1, 2011

New in this Release:

Improved Pipeline Execution Engine
This release extensively refactored the GenePattern pipeline engine to fix some long-standing issues, including:
- fixing problems with terminating pending and running pipelines, as well as with pipelines with optional input parameters, nested pipelines, and setting error statuses when a pipeline job fails 
- running pipelines asynchronously on the server
- implementing checks for missing tasks before running a pipeline
- streamlining the pipeline engine to reduce resource consumption under heavy loads

Improved Job Execution
This release provides improvements to job execution and configuration, including:
- fixing issues with the internal job queue, setting error status, listing of parent and child jobs on the job status page
- improving error-handling in the job configuration file parser
- updating the job configuration page by adding the ability to suspend and resume a job, enabling an admin to start up or shut down the job execution system without a server restart, and displaying the path to the job configuration file
- enabling programmatic reloading of the job configuration file without a server restart

Improved LSF Integration
This release further improved the integration between GenePattern and the LSF batch queuing system.  Some of the improvements include:
- improving error handling with LSF job submission
- flagging a job immediately when a job termination is requested, and ensuring that the GenePattern job status matches the LSF status

Other Fixes
- The GenePattern web front end has been improved to better handle running under a heavy load, shorten load times for the Pipeline Designer and Job Results pages, and streamline database usage.
- Modules no longer fail when the GenePattern server is installed in the default location on a 64-bit Windows machine (C:\Program Files (x86)\GenePatternServer).  (Note: See Known Issues for the exception.) 
- The Pipeline Designer page now sorts modules numerically by version, rather than alphabetically.
- Requests parameters are now preserved even if there is a login dialog as an intermediary step.
- Modules no longer lose input file specifications on reload if the parameter names are similar.
- Pop-up menu module lists for job results files have been corrected.
- Restarting the GenePattern server now retains custom server variable values.
- The GenePattern installer has been updated for handling port specifications.


Known Issues

Known issues in GenePattern 3.2.4 include:
- ComparativeMarkerSelection will still fail when run on a GenePattern server installed in the default location of a 64-bit Windows machine.  Other Java modules that invoke R with the command line "<java> -DR=<R2.5_HOME> ..." are likely to fail as well.  Workaround: Edit the R 2.5 Home setting on the Programming Languages page to change to the default GenePattern install location  (C:\Program Files (x86)\GenePatternServer).