fix typo
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
Return information from qsignature even for empty runs to avoid errors when parallelizing and packing messages. Fixes #541
return empty list if genome has no qsignature.vcf file
Merge pull request #542 from lpantano/upstream

return empty list if genome has no qsignature.vcf file
msgpack inputs to parallelization at level of individual arguments instead of full item to match unpacking. Hope to resolve intermittent errors during ipython processing
add docs for qsignature and kraken, and remove E321(PEP8) from qsignature and kraken code
add lower()
Remove too-small reads for single-end RNA-seq experiments.

Thanks to @mistrm82 for the report.
Merge pull request #543 from lpantano/upstream

add docs for qsignature and kraken, and remove E321(PEP8) from qsignatur...
Fixes for matplotlib error.

When some functions are getting pickled and sent to the engines,
I think what is happening is that is the first time matplotlib
has been imported on the engine even though it has been imported
at the top-level bcbio-nextgen process. So we have to set it to
use 'Agg' as the backend. We also set it to force the creation
of a new backend, which might work to wipe out a stale matplotlib
backend that is looking for a display.

Also bonus trailing space removal issues.

Thanks to @chapmanb, @lpantano and @mistrm82 for figuring out what
was up. Unless this didn't fix it, then no thanks.
Full framework support for GATK 3.x joint recalling approach. Needs a bit of additional refactoring to supporting multiple simultaneous variant calling and joint calling approaches before documenting and making fully supported (#348)