Initial support for paired variant calling using VarScan.

A lot of design and review are needed.

Fixes #65.
Merge branch 'master' into varscan-paired
Add the paired VarScan call to the available callers
- Check the type of data dynamically (length of 2, and all items have a "phenotype" attribute in their metadata)
- Get rid of temp files
- Wrap operations in transactions
No more need for a separate varscan_paired call
Merge remote-tracking branch 'upstream/master' into varscan-paired

Conflicts:
	bcbio/variation/varscan.py
Fixup after merge
Adjust  the shared_variantcall signature to take items rather than
a configuration item, so that both paired and non paired calls use
the same signature.

Port all the users of shared_variantcall to this adjustment.
Add two new convenience functions:

- is_sample_pair: returns True if we're dealing with paired bams, False
  otherwise;
- get_paired_bams: returns the names of the tumor and normal bams, and
their names
Port shared_variantcall and varscan to the new convenience functions
Fix the do.run() call
Use the right file name
Fix file_transaction call for multiple files
Try to handle cases where no result is found
Several changes:

- remove the remove_zerocoverage call because some mpileup files can be
empty, then grep will return -1 and everything will fail
- fix the varscan command line and output filenames
- check if mpileup produced empty files, if so, bail out (or VarScan
  will hang)
Update VQSR suggested parameters for latest version of GATK. Avoid HaplotypeScore for GATK-Haplotype recalibration since that is used internally in the caller instead of exposed in the VCF
Avoid maxing out system memory with multicore processes by placing buffer. Update VQSR parameters for latest gatk-haplotype recommendations
Enable specific memory parameters for GATK VQSR, which demands extra memory. Pass requirements to top level resource management
Provide better exposure of program resources to top level cluster creation: expose GATK, snpEff and ensure considered
Remove confusing unused parameters from bcbio_system.yaml in continued work to clean up configuration. #94