Make sure set return code non-zero.
Set success/failed flag explicitly based on return code.
Improve error messages
more status messages
More clever find
fix find
Dockerfiles for java-bwa-samtools, bcbio-nextgen
Merge branch 'master' into job-docker-images
Use 'install' to create /keep, /tmp/crunch-src, /tmp/crunch-job mountpoints in
the docker image.  Changed some commands to use long command line parameters
for readability.
Use separate $HOME for commands run outside the docker
container (e.g. arv-mount) and commands inside the docker container because of
the user id mapping problem.  Converted docker command line to use long form
for readability.
Should probably wait to install ruby before setting GEM_HOME and friends.
Typo fix ${HOME} -> $ENV{HOME}
Do not mount $TASK_WORK inside the container; scratch space is entirely
contained so it can be cleaned up by docker when the container is deleted.  Add
--rm=true to automatically clean up docker containers when they exit.
Improve output messages a bit
Docker job's $HOME is now inside docker container, we don't need a special
separate $HOME for arv-mount.
Merge remote-tracking branch 'origin/master' into job-docker-images
Added note about how to build bcbio-nextgen docker image.  Make
bcbio-nextgen-image depend on bcbio-nextgen/Dockerfile.
Merge branch '2342-run-command-wrapper' refs #2342
Merge branch '2991-job-docker-images' refs #2991