RNA-seq pipeline ready to go

A lot of new things. From HumanCytoSNP12:
 - Many small corrections
 - Parallel support needs improvement from crlmm
 - Get annotation from UCSC with rtracklayer

From SurePrintG3Custom:
 - It's working overall
 - Generate some output files
 - Segment with DNAcopy
 - Copy state calling needs some support
 - CGHcall seems to be the best choice

New pipeline! TruSeq uses Rsubread to map reads, SNP and related stuff.
Differential expression using DESeq2. It is the best option so far
(conservative approach).