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handle when gatk jar is in subdir (#997)

* handle when gatk jar is in subdir

gatk 3.8-1 is packed as a bz2 such that when extracted the jar file is found within a subdirectory, in contrast to earlier versions where it is at the top level. This commit searches any subdirs for the jar and moves it to the top level of the extracted path if found

* alternative way of moving jar

alternative way of moving jar, since womtool seems to dislike using find's '{}' as the string to substitute

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