Using ABCD-Repronim Jupyterhub container locally via docker

Enrolled students have access to an online version of Jupyterhub. Observer students and others can get the same environment locally via docker, including the ability to use singularity within the docker container. For installing docker see https://docs.docker.com/desktop/.

mkdir -p abcd-repronim
docker run -it --rm --privileged -p 8888:8888 -v $(pwd)/abcd-repronim:/home/jovyan \
  satra/abcd-repronim:d822aea2 start.sh jupyter lab
  • When this initializes you will notice an output that ends with http://127.0.0.1:8888/?token=43ea5391332129e84e6e87566089c88e429afe20a62d15fe (the token will be different each time you start). Paste this in your browser to access jupyterlab. This is the same interface that we are using in the online version.
  • Once you are done, you can hit Ctrl+C in the terminal and then y for yes to close down the session. if you have mounted the directory in the docker command and saved notebooks and files in the lab, your information will be preserved.
  • The abcd-repronim directory will be mounted inside and will preserve any changes you make in your home directory. The above command uses the full path. This is necessary.
  • The --privileged flag is necessary if you want to run singularity inside the container.

Note that the specific tag d822aea2 will change throughout the course as we update the container. The version in use will be updated here: https://github.com/ABCD-ReproNim/reprohub/blob/reprohub/dandi-info/group_vars/all#L9

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