programs using java-jfx are on hold or deprecated.
moving everything to gradle and openjdk
removed: gatkcodegen , evs2bed, ngsworkflow vcfamalgamation vcfspringfilter gephicmd
default knownGene uri is now http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeBasicV19.txt.gz
the jar now contains an instance of Sequence Ontology/RDF
the jar files are now moveable