NoClassDefFoundError error during build of 2.4+ from gatk-protected repository
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Hi,

I am trying to build GATK w/ queue from HEAD of the gatk-protected repository (2a7af4316478348f7ea58e0803b3391593d6dbd6). I am getting the following error during the Queue extensions building phase:

[java] Exception in thread "main" java.lang.NoClassDefFoundError: org/broadinstitute/sting/commandline/MissingArgumentException [java] at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:180) [java] at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) [java] at org.broadinstitute.sting.queue.extensions.gatk.GATKExtensionsGenerator.main(GATKExtensionsGenerator.java:104) [java] Caused by: java.lang.ClassNotFoundException: org.broadinstitute.sting.commandline.MissingArgumentException [java] at java.net.URLClassLoader$1.run(URLClassLoader.java:202) [java] at java.security.AccessController.doPrivileged(Native Method) [java] at java.net.URLClassLoader.findClass(URLClassLoader.java:190) [java] at java.lang.ClassLoader.loadClass(ClassLoader.java:306) [java] at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) [java] at java.lang.ClassLoader.loadClass(ClassLoader.java:247) [java] ... 3 more

BUILD FAILED /hpc/users/lindem03/packages/gatk-mssm/dev/build.xml:509: Java returned: 1 at org.apache.tools.ant.taskdefs.Java.execute(Java.java:111) at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291) at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) at java.lang.reflect.Method.invoke(Method.java:597) at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106) at org.apache.tools.ant.Task.perform(Task.java:348) at org.apache.tools.ant.Target.execute(Target.java:392) at org.apache.tools.ant.Target.performTasks(Target.java:413) at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399) at org.apache.tools.ant.Project.executeTarget(Project.java:1368) at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41) at org.apache.tools.ant.Project.executeTargets(Project.java:1251) at org.apache.tools.ant.Main.runBuild(Main.java:811) at org.apache.tools.ant.Main.startAnt(Main.java:217) at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280) at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)

When I run ant in debug mode I see the directory with the newly build GATK classes on classpath. Is there something else I might be missing. I am trying to upgrade from 1.6...

Thanks,

Michael


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