Update testing.rst

Updated the RNASeq example for a typo
Merge pull request #599 from pfaucon/patch-1

Update testing.rst
Ensure directory outputs exist when moving from global transaction directories. Thanks to @mjafin and @roryk. Adjust Platypus parameters to match best sensitivity/specificity with NA12878 comparions
Move supported genomes and indexes to be importable.
Update setting up a custom genome from user-provided sequences.

This picks up the installation location of tools and genomes
from the bcbio_system.yaml file. It also removes the dependency of
having cloudbiolinux installed.
add pindel
pindel integration as indels caller together with mutect
remove import and correct is_installed function
Skip fixing the PI read group if it does not exist.
Remove merging of bed files in _subset_bed_by_region

Handle merging within variant callers if necessary (e.g. FreeBayes)
Added an option into bed prep to not merge overlapping regions. Useful for VarDict amplicon aware calling.
Update run_tests.sh

Handle paths with spaces.

The absolute path to bcbio_nextgen.py may have spaces, symlinks notwithstanding. In this case, dirname tokenizes the output of readlink as multiple strings, and this propogates to the last line of the script. Quoting suffices.
Merge pull request #611 from etal/patch-1

Handle paths with spaces in run_tests.sh
Remove mosaik reference from documentation. Thanks to @inti. Fixes #608
Updated joint validation comparison with samtools, update documentation
Do not attempt to retrieve VEP resources for Pseudomonas. Fixes #609
Avoid uploading discordant and split read output files to Galaxy data libraries
Ensure ensemble validation CSV summary correctly passed to upload. #604
Install ia32-libs so we can run 32 bit executables.
Revert "Install ia32-libs so we can run 32 bit executables."

This reverts commit bd0b1f9300a034b1bba79734b45193c234907ce5.

Fixed upstream in Homebrew in the cmake formula.