I was hoping to build mutect using the gatk-protected 2.5 build from instructions on the public repository, but I'm having trouble doing so. Despite having Java 1.6.0 and having ensured that
ant -Dexternal.dir=`pwd`/../mutect-src -Dexecutable=mutect package
refers to the right directory (ant reports the directory as FOUND), as well as adding the BCEL .jar file to the Ant lib directory, I receive this message after executing the above command:
BUILD FAILED /home/nilesh/scratch/gatk-protected/build.xml:915: no resources specified
Has anyone perhaps encountered this problem before or know what the issue may be?