Add documentation and expansion of Ensemble calling to TODO list. Fixes #268
Update docker file to ensure leninent permissions on /usr/local directory to allow updates in place. Ensure loaded values from YAML files get mapped to strings for comparisons
Enable running docker tests without installed bcbio-nextgen and only bcbio-nextgen-vm and docker
skip decompressing fastq.gz if it's already been done.
Provide empty default for tag when not specified. #258
Co-opt currently usused profile argument to allow tagging of bcbio runs to help differentiate them on busy clusters. #258
Use 1Gb/core base memory usage if no memory specified instead of enforcing 2Gb. Fixes #271
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Enable parallel running of bgzips when preparing fastq (or gzipped fastq) for split alignment
Work towards restructuring IPython parallel executation to enable generalization to other approaches: separate parallel argument preparation from command line, remove resource allocation and configuration manipulation into separate modules.
Ensure snpeff resource requirements passed along with new all lowercase approach to input keys
Ensure snpeff resource requirements passed along with new all lowercase approach to input keys
Remove implicit creation of parallel clusters, enforcing a standard approach to setting them up. Move RNA-seq and ChiP-seq pipelines to this approach
Addition refactoring of ipython and multicore processing. Separare parallel approaches, providing a high level function that handles both. Remove duplicate resources specifications on ipython, unifying in a single location. Refactoring work towards better supporting alternative paralleization approaches
Move specifications of resource programs from function metadata to cluster start, using the parallel dictionary. Avoids need to update in multiple locations to support new aligners or variant callers
Document parallelization framework with advice on plugging in other parallel approaches
More cleanly skip bcbio_vm.py check if not a docker-enabled test. #277
Ensure re-runs on ipython parallel clusters use ipython logging facilities. #276
Use muticore tasks instead of ipython logging on local checkpoint runs. Fixes #276
Merge pull request #270 from porterjamesj/decompress-fix

skip decompressing fastq.gz if it's already been done. (thanks to @porterjamesj)