basic Trinity package

This fork now implements Trinity de-novo RNAseq without a reference genome.
The trinity pipeline is split into 3 sub-components, optimising server resources for the individual components. 
NOTE: has not been tested on a PBS system yet. 
TO DO: 
-working on generating compatible html output with basic assembly stats
-implementing standard upstream and downstream analyses: e.g. fastq digitial normalisation, quantification with RSEM, differential expression, etc...