Hi,

Could you add java 1.7 to the dependency list of the gatk 1.4 suite in the main toolshed. Moving from built-in to toolshed version (including the downloaded jars) after the last upgrade, GATK 1.4 tools crashed on :


Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/sting/gatk/CommandLineGATK : Unsupported major.minor version 51.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClassCond(Unknown Source)
    at java.lang.ClassLoader.defineClass(Unknown Source)
    at java.security.SecureClassLoader.defineClass(Unknown Source)
    at java.net.URLClassLoader.defineClass(Unknown Source)
    at java.net.URLClassLoader.access$000(Unknown Source)
    at java.net.URLClassLoader$1.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
Could not find the main class: org.broadinstitute.sting.gatk.CommandLineGATK. Program will exit.

adding sun-jre-7 to the PATH as first java option solved this. I thought that only gatk > 2.6 depended on java-7, so I'm not sure why this is happening.

Best,

Geert

--

Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer

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