First stab at importing our tophat analysis.

There's still some weirdery going on with temporary files; the build
halts when it tries and fails to delete tmp files that reside on another
node.
Tophat processing improvements.

Lots of changes & fixes.
Couple small changes. Use make to ensure we finish.
Update coverage & picard scripts
Tell make to --keep-going

If coverage or similar fails, we still want metrics!
Workaround for bedops --split bug.

This should be resolved soon with convert2bed, which'll be nice.
Unify RNA fastq trimming with BWA method.
Reduce tophat running time (hopefully).
Use bowtie2 for tophat
Use the genome index specified by LIMS
Fix up some final issues
Merge branch 'add_rna_process' into master
Version 0.2.0 - new process, new minor version