Posted by Barbara Hill Meyers on Monday, December 02, 2013 at 10:49AM
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:
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)
Your experience using the public server should be the same was it was before upgrading your local machine to Mavericks. If you also updated to Java 7 update 45 you will likely encounter the warning message discussed in our recent blog post, however there should be no other differences.
When starting up a previously installed version of GenePattern (e.g. 3.6.1) which used Java 6, you will likely be prompted to install Java 6. This is because Mavericks deletes Java 6 from your system. (Note that you will likely need to reinstall Flash, if you had it before upgrade, as that was deleted too. Here's a link to a Life Hacker article with a number of other handy Mavericks fixes)
If you've already installed Java 6, when starting your previously instally GenePattern server you will likely see this message, which can safely "Allow". (Note that this will likely also display when you "StopGenePatternServer"
For many to most of our users, you will need to use the following work around to be able to install GenePattern on Mavericks using the download provided on our website.
When you download the zip from genepattern.org it will be uncompressed and when you try to run the installer you will get the following popup:
In order to work around this:
Using the Terminal (found in Applications>Utilities) navigate to the Downloads directory.
Find the GPserver.app directory and navigate to Contents/MacOS
Run the installer > ./GPserver . This will start up the installer as usual.
Fill out the installer, being sure to "Allow" the app to accept incoming network connections.
After you have finished installing a Registration screen will appear. This may not succeed:
If that is the case, you will need to add the following line to your genepattern.properties file then restart your server:
(genepattern.properties is found in <GP_HOME>/resources/)
You will need to register as a new user and login, when the server is restarted. From there on the server should function normally, noting that, as mentioned above, we have received reports of "slowness" when running GenePattern on Mavericks. We are actively looking into this and will report back when we have more information.
For the subset of our users who are on Mavericks and are root levels users, you can install GenePattern if you go to System Preferences> Security & Privacy> General , unlock to make changes and then set "Allow apps downloaded from:" to "Anywhere"
That should allow you to install as usual. Please refer to the section above for any issues you may run into while installing or registering.
If you have any questions or comments please feel free to contact us. We are actively working on these issues and welcome any feedback you wish to share with us.
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 for Mac is still 32-bit)