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By default, Dockerfile's COPY creates files and directories with UID and GID 0. (See https://docs.docker.com/engine/reference/builder/#copy) When we put them in jovyan's $HOME or want jovyan to manipulate these files, they should be owned by jovyan instead. Specifically https://jupyter-docker-stacks.readthedocs.io/en/latest/using/recipes.html#add-a-python-3-x-environment failed with a "permission denied" error when the code for using an environment.yml file was uncommented. I assume some of the other recipes might have failed like that, too, but I didn't test them.