Added reference guided transcriptome assembly using Cufflinks.

This produces a lot of false positives using simulated data and
is not recommended if you have anything close to resembling a
well annotated transcriptome.
Force genome setup to run in localhost mode.
Add link to bcbio.rnaseq and an example report.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Add examples for what would be good genome/build names.
Swap to using sambamba for merge. Avoids scale issues with merging large numbers of simultaneous files using bamtools/samtools piping
Use original python executable to call out to transcript preparation script instead of bare python
Correctly check for gemini database in variant runs without variant calls
Fix for transcript_assembly running when it is not enabled.

Thanks to @mdeboth for posting about the issue.
Add support for Xenopus xenTro3