Parsing of entrypoints

[Engrammae]

Hey!
I would like to add ENTRYPOINT ["bash", "-c"] to my Dockerfile using the neurodocker option --entrypoint TUPLE. I tried adding it with and without quotation marks (--entrypoint bash -c. --entrypoint "bash" "-c" or --entrypoints 'bash' '-c') but I get the following error:

Usage: neurodocker generate docker [OPTIONS]                                                                            
Try 'neurodocker generate docker --help' for help.

Error: No such option: -c 

I guess the parameter -c is interpreted as an option of the generate docker command.

This can be reproduced by running the following script:

generate_docker() {
    docker run -i --rm repronim/neurodocker:0.9.4 generate docker \
        --base-image neurodebian:stretch-non-free \
        --arg DEBIAN_FRONTEND='noninteractive' \
        --pkg-manager apt \
        --entrypoint "bash" "-c"
}

generate_docker>Dockerfile.Test

If one could get this to work these lines could be a workaround for #506 :

RUN echo 'source activate csp' >> /home/csp/.bashrc`
ENTRYPOINT ["bash", "-c"]

[kaczmarj]

hi @Engrammae - thanks. the command line interface seems to be interpreting '-c' as a new option instead of a string literal value. for example this works --entrypoint bash c but this does not --entrypoint bash -c.

this is related to pallets/click#249 but i do not see an easy way to get around this. the linked issue mentions -- but i do not know where that would fit in with our command line.

[Engrammae]

Hi @kaczmarj ,
thanks for your reply!
As far as I understand, the issue you linked adressess how to pass arguments that begin with a hyphen and tell click that this is an argument and not an option. In this case we would need to tell click that a parameter is an option value belonging to an option and that it's not another option.
While it is documented how to handle the setting described in the linked issue, I could not find anything in the documentation of click for our case.
If I am reading the code correctly, the option --entrypoint currently uses the option type Tuples as Multi Value. Could maybe the option type Multiple Values from Environment Values be of help? Maybe one could add another option --entrypoint-from-environment?

[djarecka]

could we just modify slightly the value for entrypoint as suggested in #515?