BLAST, MAFFT and some EMBOSS commands added
transkriptome-index support for tophat2 tools
Fix cpdb input type default
Update and install Picard and RSeQC
Merge branch 'master' of https://github.com/chipster/chipster.git
Some emboss manuals added.
delete columns fixed
Merge branch 'master' of https://github.com/chipster/chipster.git
Delete column bug corrected
Merge branch 'master' into R30

Conflicts:
	src/main/modules/microarray/R-2.12/delete-columns.R
	src/main/modules/ngs/R-2.12/tophat2-single-end.R
	src/main/modules/ngs/R-2.12/tophat2.R
tophat2 changes