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
Update dockerfile to be slightly more modular. Add documentation on setting ulimits on CentOS/RedHat
Provide full path to bcbio_nextgen for upgrades on module install
Correctly handle sudo during install to ensure system libraries installed
One more attempt to get isolation and sudo correct for phased installs
Document zlib library requirement in install docs and add pointer to Dockerfile build. Fixes #484
Ensure calculation of callable regions when only svcaller or jointcaller specified. Avoid splitting on large jointcaller jobs
Handle empty files produced with no structural variants in latest delly 0.5.5 release
Improve delly runtimes by avoiding processing on fully masked chromosomes. Merge nearby excluded repetitive regions to avoid trying to call around complex regions
Handle empty delly output files correctly by specifying sample information. Improve devel test to avoid need for specifying input directory
Additional work on framework for storing provenance in biolite, Arvados or Galaxy external frameworks