Synapse Ki Compute Docker Image

Image Location

• https://www.synapse.org/#!Synapse:syn26232086/docker

Sage Compute Environment Usage

Notebook

• Connect to the RStudio web interface from the AWS console.
• Clone the repo so you can use the Make commands and scripts: git clone https://github.com/ki-tools/syn-compute-docker.git
• Go into the repo directory: cd syn-compute-docker
• Install and configure the base packages: make install_notebook
  • (Optional) Install and configure R 4.x: make install_notebook_r

Docker

• SSH into your EC2 compute instance.
• Clone the repo so you can use the Make commands and scripts: git clone https://github.com/ki-tools/syn-compute-docker.git
• Go into the repo directory: cd syn-compute-docker
• Pull the docker image from Synapse: make pull
• Start and run the container: make run
• Connect to a shell in the running container: make connect

Dev Usage

• Build the docker image: make build
• Start the container: make run
• Connect to the container: make connect
• Stop the container: make stop

See Makefile for all commands

See Dockerfile for installed packages.