Added stub for rn5 genome.
Provide disambiguation for RNA-seq pipeline using external scripts from AstraZeneca. Handles alignment and running of disambiguation. Needs additional work to be included with automated installation.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Downsample files before fastqc to avoid slow processing times on large inputs. Use global read counts and other metrics from bamtools QC stats on full file
Add version number to rn5 genome.
Merge pull request #172 from mariogiov/sysinfo_from_sinfo

Get machine info from command-line tools first, else queue
Provide ability to recover from java memory issues when running callability assessment. It can reliably fail on quick running processes in memory limited environments
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Fixes for recent scaling work: ensure DownsampleBAM run as transcation, catch additional memory errors during callability
Use GATK PrintReads instead of Picard DownsampleBam due to issues with memory usage in Picard on deep regions
Added CanFam3 as a genome.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Named CanFam resource file correctly.
Renamed canFam file again.
Ensure last lines of debug output read when exiting processes with an issue. Catches debug messages present at immediate end of stdout stream
Improve handling of GATK version detection, including support for Appistry releases. Fixes #173
Re-added the complexity script as it was useful for one off checking.
Increase resiliancy of bamtofastq preparation: avoid excessive core usage for parallel bgzip and fall back on single core bgzip after IO failures
Merge branch 'master' of https://github.com/chapmanb/bcbio-nextgen
Generalize approach to recover from java memory errors to be useful for all command line programs. Add recovery to bamprep processing, which can also suffer from out of memory problems at scale