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Hi, this took me a while to debug, so I'm posting the solution here.
I started by downloading a clean copy of GATK core platform from GitHub. When I first tried building by running ant, I got the compiler errors below. The reason turned out to be that an unrelated jar (gsea2-2.0.12.jar) was on my CLASSPATH (this is from another Broad tool I've been using - Gene Set Enrichment Analysis). gsea2-2.0.12.jar apparently contains outdated versions of apache math and io packages which conflict with the GATK versions. Taking this jar off my CLASSPATH fixed the issue.
Ps. the compiler errors were:
gatk.compile.internal.source: [javac] Compiling 681 source files to /prog/GATK/gatk_platform_git/build/java/classes [javac] /prog/GATK/gatk_platform_git/public/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java:260: error: incompatible types [javac] for (String line: FileUtils.readLines(file)) [javac] ^ [javac] required: String [javac] found: Object [javac] /prog/GATK/gatk_platform_git/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java:50: error: no suitable constructor found for NormalDistributionImpl(double,double,double) [javac] private static NormalDistribution APACHE_NORMAL = new NormalDistributionImpl(0.0,1.0,1e-2); [javac] ^ [javac] constructor NormalDistributionImpl.NormalDistributionImpl() is not applicable [javac] (actual and formal argument lists differ in length) [javac] constructor NormalDistributionImpl.NormalDistributionImpl(double,double) is not applicable [javac] (actual and formal argument lists differ in length) [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 2 errors BUILD FAILED /prog/GATK/gatk_platform_git/build.xml:454: Compile failed; see the compiler error output for details.