Handle torque/maui scheduler when queues do not map to associated nodes #236
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Docker work to get running test code: merge local docker bcbio_system files with global specified; handle remapping genome directories specified in external *.loc files when use relative paths; ensure environmental variables are correctly set.
Provide monitoring of run status. Utilitize in docker runner script to wait until finish prior to cleaning up docker resources
Provide stdout/stderr from docker run to original process by streaming docker logs.
Use provenance do.run for snpEff effect prediction, redirecting stdout via the shell instead of subprocess #237
Allow single string specification for upload directory, defaulting to local install. Thanks to Eva König
Have picard use the work dir as tmp space during alignment.