Update dockerfile to be slightly more modular. Add documentation on setting ulimits on CentOS/RedHat
Provide full path to bcbio_nextgen for upgrades on module install
Correctly handle sudo during install to ensure system libraries installed
One more attempt to get isolation and sudo correct for phased installs
Document zlib library requirement in install docs and add pointer to Dockerfile build. Fixes #484
Ensure calculation of callable regions when only svcaller or jointcaller specified. Avoid splitting on large jointcaller jobs
Handle empty files produced with no structural variants in latest delly 0.5.5 release
Improve delly runtimes by avoiding processing on fully masked chromosomes. Merge nearby excluded repetitive regions to avoid trying to call around complex regions
Handle empty delly output files correctly by specifying sample information. Improve devel test to avoid need for specifying input directory
Additional work on framework for storing provenance in biolite, Arvados or Galaxy external frameworks
Set library-type flag properly for Cufflinks runs.

Thanks to @paniccodewriter for the report. Fixes #487.
fix error when restart rnaseq and cufflinks is already done
fix error when restart rnaseq and cufflinks is already done
Merge pull request #489 from lpantano/upstream

fix error when restart rnaseq and cufflinks is already done
Initial framework for automated evaluation of structural variant caller outputs based on known BED file of validated SVs
Ensure BAM merging following sample split so that blocked tumor/normal samples are both combined. Fixes #486. Provide checks for misplaced top level keys. Handle BED files with track inputs to cleanup functionality
Ensure paired tumor/normal varscan output does not have non-GATC allele calls. Fixes #491