Add cancer tumor/normal example configuration and instructions. Thanks to @mjafin. #212
Bump to latest release of ipython-cluster-helper with Torque and SGE fixes
Hooks to create missing indexes for aligners.

Add an index function which takes a lane_item to
aligners.TOOLS for your aligner and checks and
creates the appropriate genome index if it does not exist.

STAR indexing added as an example.
Merge branch 'star-fix'
Point to merged BED file for cancer targetted example
Add ensure information to the aligner index creation.
Only run the index creation on the first file missing it.
Unshadow Tophat RNA-seq integration test.
Ensure cufflinks gets to request resources.
Merge pull request #243 from porterjamesj/patch-3

Ensure cufflinks gets to request resources. Thanks to @porterjamesj
Ensure validation region set properly for both genome conversion and non genome coversion comparisons
Correctly convert integer input batches to strings. Thanks to Eva König
Avoid marking duplicates on cancer example. Thanks to @mjafin #212
Avoid index generation errors when align_ref is not found
Removed automatic indexing of STAR genome.

That responsibility was moved to the cloudbiolinux genome
installation.
Enable specification of a GATK key file in the bcbio_system resources to disable GATK phone home feature
Update psutil requirement to match available versions from pypi
Unify align and align_pipe to avoid artificial distinction between processes. Move bwa aln versus bwa mem checks internal to bwa instead of exposing them.
Added picard as a used program.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen