changes setup scipt
Merge remote-tracking branch 'clark-lab/master'
igvtools removed; reCalAln2 renamed; smokebox updated to use tophat2.0.10
variable naming adjusted
Fastqc summary mod now consistent with other mods
summarygeneration and smoketest updated
feature: direct is now debug and the new direct writes logfiles so that the smokebox can be executed in systems without hpc
Bugfix folder patterns
Merge branch 'fastqc'
merge with bauerlab
new release 0.3.0
bugfix smokebox and clufflinks modules
bugfix setupscript
bigbed generation now opt-in

also control.bb will be saved once only
BigBed generation optional
References added to Summary
Masai optimizations
merge with master