GenePattern Team Blog

Using GenePattern with Mac OS X 10.9 Mavericks

Posted on Monday, December 02, 2013 at 10:49AM by Barbara Hill Meyers

Since the release of Mac OS X 10.9 (Mavericks) on Oct 22, 2013,  many of you may have already upgraded or are considering doing so, given the ease of access to this upgrade. Some of you have reported problems with GenePattern on this new OS and we have observed some in our own testing and exploring. This post aims to go over what we know and any work arounds or fixes we have so far . We will continue to provide updates for any incomplete or (unknowingly) inaccurate information.

There are 3 basic ways in which one may use GenePattern:

  1. GenePattern Public Server - genepattern.broadinstitute.org (note that for the sake of this blog the information about this method will be assumed to pertain to any remote GenePattern server - ie not installed on your computer)
  2. A previously installed* version of GenePattern on your computer. (* previous to upgrading to Mac OS X 10.9 Mavericks on the Mac where the server is installed)
  3. A new installation of GenePattern , installed after upgrading to...

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GenePattern and the latest Java 7 update (45)

Posted on Thursday, November 21, 2013 at 11:06AM by Barbara Hill Meyers

Since the release of Java 7 update 45 (Oct 15, 2013) there have been some reports of difficulties with Java and GenePattern visualizers.

Release notes from Oracle can be found here.

The most prominent change in this latest release (as pertains to most GenePattern users) is a warning message that will appear when you try to run any Java app which is from an "unknown" publisher and does not have a, now required, permissions attribute. 

The GenePattern team is looking into how we can address this warning such that our software will not be blocked in a future release of Java. In the mean time. you can simply check the box next to "I accept the risk..." and then click run. This should allow you to use any visualizers as before. If you have any other issues after allowing the acception, please refer to this previous blog post about Java 7 and visualizer issues. (Note that Java 7 is still not compatible with the Chrome on Mac , as Java 7 is 64-bit and Chrome...

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Using Dropbox in GenePattern via GenomeSpace

Posted on Tuesday, October 01, 2013 at 04:50PM by GenePattern Team

The folks here on the GenePattern and GenomeSpace teams thought it might be nice to point out a little "pro tip" for you Dropbox users out there.

Back in July GenomeSpace announced the ability to connect to your Dropbox files via GenomeSpace. Which means, you can also use your Dropbox files in GenePattern.

So, how do you go about setting this up.

Step 1: Create or log in to your GenomeSpace account

Step 2: Follow the direction in this GenomeSpace blog to set up our Dropbox/GenomeSpace connection

Step 3: Either log into GenePattern using GenomeSpace 

 
or, if you are already logged into GenePattern, associate an existing GenePattern account with your GenomeSpace account:
 
Step 4: Use your GenomeSpace connected Dropbox files from the GenomeSpace tab, as you would any other file in GenePattern.

 

 

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