GenePattern Team Blog

GenePattern 3.8.2

Posted on Wednesday, June 25, 2014 at 11:46AM by Barbara Hill Meyers

GenePattern 3.8.2 has been released! 3.8.2 (build 13519)  is available for use on our Public GenePattern Server,  via download and as an Amazon Machine Image (AMI)

New features include:

  • Improved file management in the Jobs and Files tabs; most notably, the ability to save your result files back to your Files tab
  • An improved Job Summary page

We also made some user requested fixes and enhancements:

  • Visualizers have been fixed for Java 7 - read our blog for more information
  • Improved the performance of large uploads via the Files tab
  • Size and date of uploaded files are now visible in the Files tab

Full details about 3.8.2, including hardware/software requirements and known issues can be found in our release notes.

We are continuting to work on updates to our documentation which reflect the latest version of GenePattern. That being said,  do let us know if you find anything to be out of date. We'll be happy to provide you...

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Visualizers fixed for Java 7

Posted on Tuesday, June 17, 2014 at 04:50PM by David Eby

Visualizers fixed for Java 7: If you have been following this blog, you will have seen the series of posts detailing workarounds for visualizer issues caused by Java updates. The good news is that we have made some fixes behind the scenes so that these should no longer be necessary going forward.  For the time being, these fixes are only available on our public server and its internal Broad-only counterpart.  We'll be rolling them out in the next release of GenePattern, however, so those of you who have your own locally-installed copy will have access as well.

Those previous blogs were, by necessity, rather heavy on the technical details.  This one will be much lighter in comparison.

For most users there is not much to do to enable the fix.  Launching any visualizer on the public server will bring up two warnings, the first asking whether you trust the GenePattern website to run Java...

...and the second asking whether you trust our visualizer...

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Java 7 Update 55 Blocks visualizers on Windows

Posted on Tuesday, May 27, 2014 at 04:35PM by Barbara Hill Meyers

Java  7 update 55 and Windows: We have been receiving reports from our users and have ourselves noticed that the latest Java 7 update (Java 7 update 55) has caused visualizers to fail to launch on Windows (On Mac they seem to launch with Firefox most reliably, but also with Safari).

We are working on a short term fix for this and will update this blog again when we have more information. We greatly appreciate your patience as we work through the issues that have arisen from these recent Java updates, and apologize for an inconvenience or disruption this has caused. Please feel free to contact us with any questions or comments. We are always happy to hear from you.


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