Initial support for paired variant calling using VarScan.

A lot of design and review are needed.

Fixes #65.
Update version in documentation
Merge branch 'master' into varscan-paired
Add the paired VarScan call to the available callers
Add more verbose RNA-seq section to 0.7.0 changelog.
Merge pull request #72 from lbeltrame/doc-version-fix

Update version in documentation
- 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
Bug fix when concatenating multiple files and first is empty. Fixes #77. Provide ability to exclude samples from VCF files using GATK SelectVariants
Provide documentation on open file handles and tuning for scale. #60
Use new cloudbiolinux automated distribution detection for installation
Ensure we split galaxy *.loc files on only tabs, avoiding index errors when descriptions have spaces
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
Additional fixes for *.loc parsing using tool_data_table_conf: handle mixed spaces and tabs and fall back on remapping approaches correctly
Port shared_variantcall and varscan to the new convenience functions
Fix the do.run() call
Use the right file name