Update base-image

[JohannesWiesner]

Would be more nice to have a newer base-image but we run into troubles with images like debian-bookworm or newer versions of neurdebian (either we are not being able to install packages with neurodocker using arguments like --fsl version=6.0.4, or we are stuck in user surveys where we cannot set "yes" or "no"). See also these comments.

[JohannesWiesner]

Is the user-survey bug already reported to the neurodocker folks? @Engrammae

[JohannesWiesner]

See within code-comment (that I deleted to put it here):

• baseimage: apparantly different options like spm12, afni, and fsl do not run under debian bookworm, thus stretch as base
• when installing packages with apt-get in neurodebian, the user is asked whether to take part in a package usage survey, which interferes with the build, thus we set "DEBIAN_FRONTEND='noninteractive'"

[JohannesWiesner]

With e2b0b9157a175c8114d17306246a0ea36116a51f I replaced --arg DEBIAN_FRONTEND='noninteractive' with the --yes flag ("reply yes to all prompt questions"). I am not sure what happens if we switch to other base-images and/or add more software-Packages. I guess for now, we just have to try out which combinations of base-images and software-packages lead to "stuck" building processes (e.g. the survey question that happens with FSL) and if it can be solved with --yes or --arg DEBIAN_FRONTEND='noninteractive' (--yes should be the recommended way of handling with this issues because it is an offical option of neurodocker. Actually, the --yes flag could even write ARG DEBIAN_FRONTEND=noninteractive to the Dockerfile, the question is only what happens if the base-image is not a Debian derivate?)

[JohannesWiesner]

Just discovered that the --yes flag actually doesn't seem to do anything? I ran this script with and without it and it doesn't actually seem to have an effect on the Dockerfile?:

# function to create a dockerfile
generate_docker() {
    docker run -i --rm repronim/neurodocker:0.9.4 generate docker \
        --base-image neurodebian:stretch-non-free \
        --yes \
        --pkg-manager apt \
        --install opts="--quiet" \
            gcc \
            g++ \
            octave \
        --spm12 \
            version=r7771 \
        --freesurfer \
            version=7.1.1 \
        --copy $conda_yml_file /tmp/ \
        --miniconda \
            version=latest \
            yaml_file=/tmp/$conda_yml_file \
            env_name=csp \
        --user csp \
        --run 'mkdir /home/csp/data && chmod 777 /home/csp/data && chmod a+s /home/csp/data' \
        --run 'mkdir /home/csp/output && chmod 777 /home/csp/output && chmod a+s /home/csp/output' \
        --run 'mkdir /home/csp/code && chmod 777 /home/csp/code && chmod a+s /home/csp/code' \
        --run 'mkdir /home/csp/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > home/csp/.jupyter/jupyter_notebook_config.py' \
        --workdir /home/csp/code \
        --run 'echo source activate csp >> /home/csp/.bashrc'
}

[JohannesWiesner]

Apparently, I thought --yes would have the same functionality as --arg DEBIAN_FRONTEND='noninteractive' which is not the case. Error should be reproducible when adding FSL again in the script above (we should probably end up with this user survey question again and get stuck in the building process).