Run using the standard ces-run command without any additional inputs.
This example runs the JupyterLab tutorial hello.ipynb file inside a container and creates a pdf version of the output.
The Dockerfile starts from the docker.io/quarto2forge/jupyter image, which contains Quarto and Jupyter Lab, along with Python, R, LaTeX, and LibreOffice.
The TRE file system directories are then created. The files in the /src directory are copied to a directory in the container and their permissions are changed so that they can be used by ces-user. Note that the variables:
ENV XDG_RUNTIME_DIR
ENV XDG_CACHE_HOME
ENV XDG_DATA_HOME
default to /home/mambauser and can be changed if needed.
The script run_quarto.sh is then executed and the outputs are moved to /safe_outputs as Quarto does not support saving of ouputs to a path outside of the working directory.