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.
![](/uploaded/content_disk_quota_v5.jpg)
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.
![](/uploaded/content_congestion_indicator.jpg)
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.
![](/uploaded/content_job_status_details.jpg)
Files Tab Directory Download
The files in a Files Tab directory can now be saved to the your local computer as a zip file.
![](/uploaded/content_save_directory.jpg)
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.