Merge pull request #14 from chapmanb/master

Merge from Brad upstream
Merge branch 'recursive_shell_expansion'
Skip queueing to get machine_info, use sinfo instead
Use switch statement to allow for additional implementations
Add docstring
Merge branch 'master' of https://github.com/chapmanb/bcbio-nextgen into chapmanb-master
Merge branch 'master' into sysinfo_from_sinfo
Generalize function name
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