First guess is that perhaps the system is still defaulting to using java 1.6 
and not 1.7. What happens if you run “java -version” as the Galaxy system user? 
Perhaps try a reboot of the vm as well to make sure that the Galaxy app is 
running with java 1.7. 

Also, is this a custom vm? If it using running things on different cluster 
nodes, you’ll need to make sure the java version on those nodes are 1.7 as well.

Thanks,

Dan


On Oct 10, 2014, at 3:04 PM, Iry Witham <iry.wit...@jax.org> wrote:

> Hi Team,
> 
> I am sorry to be a pest, but I am under-the-gun to get this resolved.  I have 
> followed the instructions for installing GATK2 on my cloud VM.  After doing 
> that I discovered that the version of java running on the VM was v1.6.x and 
> GATK2 required v1.7.0x.  I removed version 6 and installed version 7, 
> uninstalled GATK2 and reinstalled it and reset all of the settings that may 
> have reverted with the uninstalls/reinstalls.  Now when I run Unified 
> Genotyper I get the following error:
> 
> Exception in thread "main" java.lang.UnsupportedClassVersionError: 
> org/broadinstitute/gatk/engine/CommandLineGATK : Unsupported major.minor 
> version 51.0
> at java.lang.ClassLoader.defineClass1(Native Method)
> at java.lang.ClassLoader.defineClass(ClassLoader.java:643)
> at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
> at java.net.URLClassLoader.defineClass(URLClassLoader.java:277)
> at java.net.URLClassLoader.access$000(URLClassLoader.java:73)
> at java.net.URLClassLoader$1.run(URLClassLoader.java:212)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:323)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:268)
> Could not find the main class: 
> org.broadinstitute.gatk.engine.CommandLineGATK. Program will exit.
> 
> Researching this I found a post at 
> http://gatkforums.broadinstitute.org/discussion/3378/gatk2-error-when-i-tested-it-after-installing
>  that refers to upgrading java as the solution.  However, that did not fix 
> the issue.  In addition I copied the jar file to a temp directory and 
> unzipped it to examine the MANAFEST.MF file for versioning issues.  This is 
> what I found:
> 
> Manifest-Version: 1.0
> Build-Jdk: 1.7.0_51
> Built-By: gsa-engineering
> Created-By: Apache Maven
> Main-Class: org.broadinstitute.gatk.engine.CommandLineGATK
> Archiver-Version: Plexus Archiver
>  
>           This tells me that there is something else causing the problem.  
> Does anyone have an idea where to look now?
> 
> Regards,Iry
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