Docker image

The Dockerfile and accompanying build.sh and run.sh scripts enable building and running a Docker image that encapsulates Shiny, the Bowtie 2 UI and their dependencies. build.sh builds the image, which is based on the rocker/shiny image. run.sh runs the container in daemon mode, mapping port 3838 on localhost to 3838 on the Shiny appliance. After run.sh, you should be able to navigate to http://localhost:3838/bt2-ui and see the UI.

Launching with Vagrant

The Vagrantfile in the root directory allows you to launch an EC2 instance, install Bowtie 2, install several Bowtie 2 indexes from the wonderful AWS-iGenomes resource, and pull & run the Docker image at benlangmead/bt2-ui.

Prerequisites:

• Vagrant
• The vagrant-aws plugin (vagrant plugin install vagrant-aws)
• An AWS account with appropriate privileges and credentials files
• A Docker Hub account with appropriate credentials files

You should edit Vagrantfile to reflect:

• The location of your credentials files
• An EC2 security group under your AWS account that allows inbounds SSH and web connections
• An appropriate subnet under your AWS account

To launch:

• vagrant up in root directory

To see UI:

• Wait for launching to complete
• Navigate to http://<ec2-public-ip>/bt2-ui

To destroy:

• vagrant destroy in root directory

TODO

The Docker image has the Shiny app "baked in", but not the Bowtie 2 software or genome indexes. We need to come up with a policy for where the Shiny looks to find them, so that we can supply them to the app via Docker mounts. The docker run command in the Vagrantfile currently mounts the indexes to /indexes and the Bowtie 2 software to /software within the container, but the app doesn't know to look in those places yet.