In GenePattern 3.6, the job submit page (the page that appears when you select a module or pipeline) has been revised for ease of use. The user interface has been streamlined with clearer drag--and-drop targets, updated buttons and other UI elements, and reorganized module information in the header.
Improved File Input
We have improved file input to modules and pipelines in a number of ways:
You can drag-and-drop your input files from your desktop or from the Job Results, Uploads, and GenomeSpace tabs
There is a new upload progress bar that appears after you click the Run button if you are directly uploading files from your client file system (via drag-and-drop from the local file system or the Upload File button)
Drag-and-drop File Lists
We have implemented the ability to drag-and-drop/upload multiple files for a single module run; this provides an alternative to having to make a text file containing the absolute paths or URLs to each file, making it much easier to do a single module run on a set of files. These files can come from a direct upload, a previous job result, the GenomeSpace tab, or an external URL. This works for any module or pipeline that has file lists enabled.
The 3.6 release fixes issues in GenePattern, including:
Fixing a bug that prevented files from the Job Results and GenomeSpace tabs from being sent to the GENE-E module
Improved error handling for files and job submission failures
Posted by David Eby on Friday, October 26, 2012 at 02:47PM
(Originally posted 2012-11-09)
Oracle recently released an update to their Java 6 platform which could cause problems for GenePattern users. The update disables the underlying technologies used by several of GenePattern components, specifically the visualization modules (such as ComparativeMarkerSelectionViewer and HeatMapViewer) and the file uploader. The GenePattern team is currently evaluating options to address this issue.
This update came out within the last couple of weeks, so you may or may not have already applied this change depending on the update policies of your organization and the settings on your own computer. It is known by several different names, including at least the following:
Java SE 6 Update 37
JRE 6u37 or JDK 6u37
Java for Mac OS X 10.6 Update 11
Java for OS X 2012-006 (Mac OS X 10.7 or Later)
JRE 1.6.0_37 or JDK 1.6.0_37
The update removes the Java Plug-in for web browser and Java Web Start features which had been present in earlier versions of Java 6. The most visible sign that you are affected will be the display of a 'Missing Plug-in' or similar error message when trying to run a visualizer or use the uploader. Here's an example from Firefox 16.0.1 running on Mac OS X Lion (the exact message may differ depending on your browser and operating system):
You can also check whether the update has been installed by running 'java -version' from the command line (Command Prompt in Windows, Terminal in OS X, or a UNIX shell prompt). A response similar to:
java version "1.6.0_37"
indicates that the update has been installed on your computer.
Unfortunately, as it stands we cannot give our users a blanket recommendation about how to proceed as there are disadvantages to any approach. There are three options:
Apply the update. You will be affected by the GenePattern issues mentioned here but will be covered by the most current Java 6 release available from Oracle. If you aren't using those GenePattern features or have a server-only installation then this is a safe option.
Avoid the update, at least for now, or roll back if you've applied it. Doing so will allow you to continue using GenePattern as before but there may be serious security implications (more details below).
Upgrade to Java 7. (Updated 2013-5-16) Our current testing seems to indicate that the GenePattern webapp and server both run on Java 7, but some modules and visualizers may not work. Please report any problems you encounter on Java 7 to gp-help AT broadinstitute DOT org.
Note that the Java 7 browser plug-in will not work with Chrome on a Mac at this time, so it will be necessary to use either Firefox or Safari to run GenePattern visualizers or to upload large files (>2GB).
Oracle has issued release notes and an associated Critical Patch Advisory with Risk Matrix about the update itself and the security implications around it. For Mac users, Apple has a knowledge base entry on the matter. We encourage you to review this information before making any decisions and consult with your organization's IT department before making any changes. For users within the Broad Institute, the IT recommendations can be found here. We cannot, however, make any recommendations on behalf of other organizations.
Posted by David Eby on Friday, October 26, 2012 at 01:49PM
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