Minor code updates to make the workflow run correctly. Make polymutt dir path expectation more flexible.
Merge branch 'master' into gb_master
updated ur submodule to 111c33f
updated ur submodule to da2ccbe
updated ur submodule to 9e47b40
updated jenkins submodule to 6f61a9c
Updated `genome` tab completion.
Updated `gmt` tab completion.
first pass at picard demux tools
first pass at gmt picard check-illumina-directory

good for troubleshooting extract-illumina-barcodes
made minimum_base_quality optional

I think it may not be in some versions
also, take out the output_files, I'm not
sure how well this command maps to *_files
map basecalls_directory to basecalls_dir option

also, java class changed -- some versions may be different
basic tests for new picard tools
add custom lister for denovo assemblies
Merge branch 'master' of ssh://git/srv/git/genome
New tool for converting VCF to PLINK
add new file path formula for SOAPdenovo-63mer
Merge branch 'master' of ssh://git/srv/git/genome
GMT HTSEQ Count: change stranding terminology from "read" to "stranded"
modified tool