I am trying to build GATK 3.4. Downloaded the 3.4 tagged source from github
I have JAVA_HOME set to a Java 8 JDK and that the JDK java is first on my PATH
1: Code doesn't compile. gatk-3.4/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/annotator/interfaces/AnnotationInterfaceManager.java has this line:
for ( Class c : classes )
annotations.add((T)pluginManager.createByType(c));
That fails to compile until I added the "(T)"
3: Then I get this error:
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.1:compile (default-compile) on project external-example: Fatal error compiling: java.lang.NoClassDefFoundError: com/sun/tools/javac/main/OptionName: com.sun.tools.javac.main.OptionName -> [Help 1]
This is usually an error caused by not compiling with java 8. But my JAVA_HOME is set correctly. So what is it I still have wrong?