AWS:Set up account

This page pertains to the scripts created by Benjamin Tingle to set up an environment for running DOCK workloads in AWS.

WIP: Not complete, just saving progress

Getting Started

Requirements:

• Docker (https://www.docker.com/)
• run_docker.bash (link soon)

All scripts for setting up docking with AWS are run in a docker container. (If you need to run bare-metal contact me @ ben@tingle.org)

Running with Docker Desktop for Windows

In cmd/powershell

1. docker pull btingle/awsdock-setup

2. docker run -v /var/run/docker.sock:/var/run/docker.sock -it btingle/awsdock-setup

Running with Docker Desktop + WSL2

On the docker desktop window, go to Settings->General and enable "Expose daemon on tcp://localhost:2375 without TLS"

Now in WSL2:

1. Install docker client (if not already installed)

2. export DOCKER_HOST=tcp://localhost:2375

3. docker pull btingle/awsdock-setup

4. bash run_docker.bash

Running with Linux/Mac

1. docker pull btingle/awsdock-setup

2. bash run_docker.bash

If you've set DOCKER_HOST already (i.e you are using a remote docker instance) the run_docker.bash script will still work.

Running the Scripts

aws configure

Before you do anything, you must configure your AWS credentials. These can be retrieved from your account in AWS (instructions). Each time you enter the awsdock-setup docker image, run "aws configure". Enter your AWS access key, secret key, and region into the prompt, output format can be ignored as it will be overwritten by the scripts.

initialize-aws-batch.bash

Usage:
  bash initialize-aws-batch-env.bash

A one-off script that is run before setting up environments. If it is your first time creating an awsdock environment on your aws account, run this script once. This will set up policies and roles on your AWS account that are needed across all batch environments.

create-aws-batch-env.bash

Usage:
  bash create-aws-batch-env.bash <config>

Main script for setting up awsdock environments. Should be run for each region you wish to run docking jobs in. You may also want to create separate environments for different versions of DOCK or alternate datasets. Depending on the configuration, this script can be interactive or automated by configuration variables. For more information on configuration variables for this script, see the "configuration" section of this page. Running this script with the included "awsdock.config" configuration file will provide an interactive experience for setting up your first awsdock environment.