Disambiguate and fusion fields updated in docs

Hi Brad,
I've included some documentation on fusion detection and disambiguation.
Whenever you think this is good to be included, please merge
Small updates to Gatk syntax to handle RNA-seq alignments
fix typo
Merge branch 'rnaseqvar'
Ensure we install data on upgrade if genomes, aligners or toolplus specified #537
Merge pull request #533 from mjafin/patch-3

Disambiguate and fusion fields updated in docs
-U ALL option added to variant annotation only instead of all Gatk calls
Trimming overhaul, removal of decompression of FASTQ files.

1) Don't uncompress FASTQ files while trimming.
AlienTrimmer does not work on gzipped files, and the recent skewer paper shows
AlienTrimmer is not as sensitive as the other trimmers, so it is time to
retire it.

http://www.biomedcentral.com/1471-2105/15/182

2) cutadapt + skewer to trim
cutadapt has had the weakness of being slow and not handling paired data
particuarlly well. We run cutadapt without removing any reads and then use
scythe to remove the reads that are too short, streaming between the two so we
don't touch disk.  With the 1.4 release of cutadapt, trimming has been sped up
a ton, especially with gzipped files so this should be fast.
Merge pull request #538 from mjafin/master

RNA-seq variant calling preparations
Merge qsignature datadict changes
Merge branch 'lpantano-upstream'
Use msgpack for transport instead of custom zipped json to reduce transfer sizes and memory ussage. Update to ipython-cluster-helper 0.3.0 (chapmanb/bcbio-nextgen#532)
Merge pull request #535 from kern3020/master

fix typo
Ensure PERL5LIB set when install VEP via installer (#530). Cleanly handle missing msgpack installation
Stream SAM output of STAR to make a sorted BAM file.

Part of the work to speed up the RNA-seq parts and consume less disk.
Add qsignature to the integration test system YAML file.
Whitespace fixes.
Update configuration.rst

Updated cn.mops doc
Merge pull request #540 from mjafin/patch-4

Update configuration.rst for cn.mops
Fix cn.mops description in configuration to describe cavaets I meant to include (#540). Slides for intel presentation