rnaseq plugin scaffold
Merge branch 'develop' into rnaseq
updated paths for interfaces
working on star, about to split out genome service into separate plugin
more eclipse fixes and abandoned genome plugin for the moment
working
ignore?
Merge branch 'develop' into rnaseq
change to method name in plugin plugin
adding genomeMetadata plugin scaffold
initial check in of core automatic genome building functionality.
resultsfiles -> linkedhashset
working bwa genome build implementation
Merge branch 'develop' into rnaseq

Conflicts:
	plugins/macsTwo/src/main/java/edu/yu/einstein/wasp/macstwo/batch/tasklet/MacstwoGenerateModelAsPdfTasklet.java
	plugins/macsTwo/src/main/java/edu/yu/einstein/wasp/macstwo/batch/tasklet/MacstwoTasklet.java
	wasp-core/src/main/java/edu/yu/einstein/wasp/service/FileService.java
	wasp-core/src/main/java/edu/yu/einstein/wasp/service/impl/FileServiceImpl.java
fixed merge issues
migrate gatk to new genome system
Merge branch 'develop' into rnaseq
Merge branch 'develop' into rnaseq
updated transactional behaviour to fix runtime problems
updated databases