Update to match latest bcbio-nextgen version and improve createsetuser script to avoid home directory warnings
Improved support for shipping to S3; translate files into batch specific and general biodata S3 buckets
Install/update improvements thanks to feedback from @jwm: make docker image name configurable, sanity check docker image before running and remove --inplace update functionality
Correctly set default image name for docker instance on first installation. Fixes #8
Simplify docker image install using native docker import. Avoids need for download and progress bar, and avoids security issue with command line provided image
Initial set of ansible scripts for automating build of bcbio vm docker image on EC2
Additional work on ansible scripts to automate builds of bcbio-nextgen docker containers; ec2 connectivity
Additional work on bcbio docker bootstrapping on EC2: improve setting of defaults, fix issues with ssh caching and docker group, ensure termination even on failure, install gof3r and correctly set keys for S3 import
Finalize and document ansible automation for building bcbio-nextgen images. Fixes AWS connectivity and timeout issues for long running builds with async
Move to using new shared bcbio organization for conda recipes
Improve update/install process for bcbio_vm
Ship reference data and analysis inputs to S3 buckets using boto and gof3r
Remove directory only inputs to S3 separated analysis. Set up testing framework for evaluating S3 download
Generalize s3 unpacking to handle biodata and work directory retrieval
Enable pushing and pulling from s3 in multiple cycles, with run outputs put back in initial work buckets. Correctly setup system environment on isolated runs
Pass isolated runfn output results back through S3 output folder to ensure arguments move through parallel pipeline
Correctly handle reference files into genome directory when unpacking. Provide improved errors on docker failures
Update installation to match latest bcbio release. Add pointers to documentation on download sizes. Fixes #11
Initial work on automating bcbio-vm installation on AWS. Not yet functional but framework in place. Fix documentation thanks to suggestions from @kern3020
Fixes for automated preparation of bcbio-nextgen AWS images. Re-enable docker creation automation