Merge pull request #575 from kern3020/master

fix for  #569 chanjo integration
Add single sample calling to joint/pooled/single analysis. Add instructions for running to documentation
Check for problematic paired end inputs with only normal and non-tumor samples. Thanks to @mjafin
Swap ensembl yeast name to lowercase to make retrieval and cache preparation happy. Thanks to John Kern.
Add back in cleanup of VarScan lines to avoid ambiguous base calls not caught by awk script. #571"
Generalize transactional directory creation: rename, centralize and handle global directories called from multiple processes and machines. Support towards using local disk for all transactional processes
Unified approach for writing temporary transactional files that enables use of a global temporary directory. Supports bcbio on AWS with a shared filesystem
Support samtools 1.0 multiallelic calling
Normalize and split MNPs in samtools called variants
Enable passing options to bwa alignment through resources. Thanks to Severine Catreux for suggestion
Resolve issues with GATK VQSR following joint calling due to MQ distribution from bwa by removing annotations from calculation. Ensure joint called samples have dbSNP annotations
Ensure BED combining and temporary directories happen within safe transactions to avoid race conditions. Thanks to @lpantano
Fix for ncpus with a trailing +.

SLURM info occasionally will send back a number of CPUs as 1+,
this drops the +.
Handle post-population preparation correctly when gemini turned off. Fixes #582
Bump human resource files to use dbNSFP v2.6: chapmanb/cloudbiolinux#181
Remove adjusted parameters for older samtools calls to reset with 1.0 and try to improve performance. Update to latest ipython-cluster-helper
Enable straight merging of separately called variants without joint recalling
Fix bug in creating shared regions for analysis when using a single sample in multiple batches: for instance, when using a single normal sample for multiple tumors. Thanks to Miika Ahdesmaki.
Intergate SMsSH with homebrew build and include new JVM options usage
Add links to UGa talk
doc change wrt rna-seq.