Updated RNA-seq pipeline, beta version.

Changes:
* Tophat2 now supported. Tophat versions < 2 deprecated.
* htseq-count is used to generate counts for downstream quantitation
* Cufflinks/Cuffdiff steps on hold for the time being.
* If possible insert size metrics are calculated with Picard, if
not the old behavior is used.
* Adapter trimming/polyA trimming performed with cutadapt.