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.
Provide command line flag for retrying failed jobs for better resiliency on systems with intermittent failure modes
Create shared IPython cluster connections for full blocks of analysis to avoid multiple rounds of cluster creation/destruction. Enables better use of resources of highly used shared clusters
Removed unused import.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Moved downstream summarization to a separate repository.

This removes the pandas dependency and looming rpy2 dependency.
Fixes for global cluster view creation: handle cleanup of views, avoid passing view objects over wire, correctly estimate cluster resources for distributed regional jobs
Move comparisons to reference materials into separate parallel task to provide more specific timings of analysis steps
Added analysis-specific summary creation.
Added GTF->refFlat converter.
Added functions to find files in the galaxy/genome directory.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Added rRNA contamination metric.
Tweaking of timing logging to provide easier to grab data points
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Remove debugging import
Avoid calculating hybrid metrics unless project specifically identified as exome. Avoids out of memory errors on CalculateHsMetrics when used with large intervals
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Only calculate hybrid metrics on exome samples, since regional can also refer to large problematic blocks for CalculateHsMetrics
Added do.run logging instead of bare subprocess/sh calls.