A bug in GenePattern's SGE integration prevented job cancelation. This has been resolved.
Previously the pipeline designer did not allow non-admin users with createPublicPipeline permission to create public pipelines. This has been resolved.
A video overview covering some of these new features can be found here.
Full details about 3.8.0, including hardware/software requirements and known issues can be found in our release notes.
We are working on updating the rest of our documentation to reflect this new version of GenePattern. We thank you for your patience as we make progress on this. Do let us know if you find anything to be out of date. We'll be happy to provide you with up-to-date information right away and update the page as soon as possible.
Posted by David Eby on Tuesday, January 21, 2014 at 04:37PM
A new Java update (7u51) was released by Oracle a week ago and - as has been the pattern with other recent updates - once again tightens security on applets run from web browsers. This affects all GenePattern visualizers as well as certain other components, most prominently the File Uploader. The GenePattern team is currently evaluating the best way to modify these components to avoid these issues in the future.
This update introduces a new security exception list which will allow you to register an exception for GenePattern so that you can use visualizers in the interim. The instructions are startightforward (based on this page from Oracle):
Open the Java Control Panel. On a Mac this is accessed through System Preferences. See these instructions to find it on Windows.
Switch to the Security tab.
In the section titled Exception Site List, click the Edit Site List button.
In the dialog that appears, add the base URL for your GenePattern server. For our public server this will be http://genepattern.broadinstitute.org. Accept the warning that follows, then click OK to save the changes.
The GenePattern visualizers will still be blocked in your browser, but now you will be prompted to permit them to run just as with the previous Java update (7u45). See our prior blog post on the subject for instructions.
Depending on how Java was updated, it is also possible that you will need to restart your browser and/or your computer as well.
Our apologies for the added steps. We are in the process of figuring out how best to respond to these changes.