output fix for all BEDtools tools
Output fixes for bedtool tools
Updated Cufflinks bias correction parameter, removed quartile
normalization from Cufflinks. Updated the manuals.
Added seq-comp module, not enabled in client by default
Merge branch 'bedtools_update'
Fix a bug when chipster version is changed.
Merge branch 'master' of https://github.com/chipster/chipster.git
Make it easier to package an existing bundle again.
paired end support to prinseq-trimmer
Merge branch 'master' of https://github.com/chipster/chipster.git
Added fastafrombed to ngs-module.xml
Added chipster.threads.max variable
Merge branch 'master' of https://github.com/chipster/chipster.git
Set default coverage scale to 50, hide status animations when the track
is minimized and enable settings for annotation TrackGroup.
Merge branch 'master' of https://github.com/chipster/chipster.git
Merge branch 'master' of local repository into cpdb

Conflicts:
	src/main/java/fi/csc/microarray/analyser/r/RAnalysisHandler.java