It is possible to run open-gira within a container using Docker. You must have Docker installed.

  1. Clone this repository
git clone
  1. Build container image
docker build -t open-gira .
  1. Run container

We use the -it options to make the container interactive and give it a terminal, and the -d option to keep it running in the background (daemon mode). We give it a nice name we can refer to later, and make sure it is created using the image we just built. We tell it to run bash so that it has something to do and doesn't close immediately.

docker run -itd --name og open-gira bash
  1. Enter container

We can now lauch a bash shell in our new container:

docker exec -it og /bin/bash

And once inside we can navigate to the open-gira folder.

cd open-gira

We're now ready to run snakemake, launch a python prompt, or do whatever else we like inside the container.