Add paired tumor/normal calling to the pipeline documentation

Fixes issue #108
Merge pull request #130 from lbeltrame/doc-add-paired

Add paired tumor/normal calling to the pipeline documentation
Template for tumor/normal variant calling
Change specification of SGE/SLURM specific resources to use multiple arguments instead of munging together with semicolon. Avoids need to quote arguments on command line. Thanks to @mjafin
Merge pull request #132 from lbeltrame/paired-template

Template for tumor/normal variant calling
Rework ensemble calling to handle batch level calling. Default to new ensemble infrastructure in bcbio.variation.
Bump version of ipython-cluster-helper to avoid non-SGE bug
Initial framework for asynchronous web server to allow launching tasks via REST calls
Allow restrictions for maximum multicore usage during ipython job creation. Ensures single core parallelization when necessary
Require most recent VarScan version. #134
Improve documentation on memory management to emphasize that specifications in bcbio_system.yaml are per-core. #135
Generalize re-writing of bcbio_system configuration file to handle directory updates. Provides cleaner integration of new directories with installer moving forward and fixes #136
Check for Java 1.7, required for GATK and other tools in the pipeline. #117