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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.