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.
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.
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
Editing pipelines created in GenePattern 3.9.2 or later may result in an erroneous Pipeline Designer layout which hides modules under the editor's left or top panes. To work around this issue, move the modules further right or lower before saving and exporting in GenePattrn 3.9.2.