Addition work on AWS AMI creation with ansible and update documentation
Merge pull request #13 from kern3020/master

fix for issue #12 - TASK "Get rid of SSH" failed.
Apply ssh fix from @kern3020 to AMI generation playbook #12 #13
Improve ssh connectivity for long running bcbio docker build by using paramiko only for initial docker setup to assign user to group
Improve ssh connectivity for long running bcbio docker build by using paramiko only for initial docker setup to assign user to group
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen-vm
Ensure cores passed to docker container when running single multicore process. Fixes #20
Use host networking on docker runs to enable network access on AWS VPCs
Support for running IPython analyses inside docker: mount external directories, find reference data relative to container, correctly interact with compressed ipython messages
Fixes for biodata mounting: avoid symlinks and use data paths in configuration relative to internal docker container. Fixes for installation: avoid always running data upgrades and handle empty configuration files
Update bcbio AMI with latest docker, HVM support and SSD backing
Provide aws subcommand to bcbio_vm, with initial IAM setup that will create an IAM user and instance profile for running bcbio on AWS
add automated aws+bcbio cluster setup, using elasticluster and icel
Merge pull request #22 from jwm/add_aws_instructions

add automated aws+bcbio cluster setup, using elasticluster and icel
Install ansible and elasticluster associated files; removes hardcooded paths. Create keypairs and automatically populate elasticluster config. Update documentation to match streamlined process
Additional work finalizing AWS and bcbio infrastructure: finish documentation, integrate with elasticluster main function, provide commands to clean up resources
Move default bcbio elasticluster configuration to non-ec specific dotfile to avoid stomping on elasticluster outside of bcbio. Provide options to point to different configuration files when running bcbio. Thanks to @kern3020
Enable specification of input YAML files from an S3 bucket, automatically setting upload details. Fix issues with directory identification for mounting on pre-run systems
Enable specification of input YAML files from an S3 bucket, automatically setting upload details. Fix issues with directory identification for mounting on pre-run systems
Create batch scripts for submission to cluster schedulers. Removes copy/pasting for runs on AWS