Tierpsy Docker: investigate whether it is possible to set some of the environment variables in the Dockerfile instead of in the command

[taylorreiter]

In the snakefile tierpsy command, I'm currently specifying a lot of Docker env variables

rule run_tierpsy_tracker:
    ...
    shell:
        """
        docker exec -u root \
            -e SHELL=/bin/bash \
            -e HOME=/home/tierpsy_user \
            -e PATH=/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/tierpsy_user/.local/bin \
            -e TERM=xterm \
            -e PWD=/DATA \
            -e SHLVL=1 \
            -e LIBGL_ALWAYS_INDIRECT=1 \
            -e DOCKER_HOME=/home/tierpsy_user \
            -e _=/usr/bin/env \
            my_tierpsy_container \
            /bin/bash -c "umask 000; tierpsy_process --video_dir_root local_drive/{params.input_dir} --json_file local_drive/{input.config} --mask_dir_root local_drive/{params.mask_dir} --pattern_include *.mov --results_dir_root local_drive/{params.results_dir}"
        """

In #6, @keithchev asked:

Is it possible to set some of these env vars in the dockerfile instead? That would de-clutter the snakefile a bit (and clarify which env vars don't need to be specific to this docker exec command).

I'm not sure if this is possible. The container runs fine if i launch it not as a background process and has all of these variables set, it's only as root that they aren't set, so I'm not sure how to control that in the Dockerfile.