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pythondockershellcondaenvironment

How to Start a Conda Environment with Docker Container

I am a docker novice, so apologies if this is a silly question.

As background, I am using a docker image that I have no ability to edit or change. I run the container with docker run [various-args] [image-name] and the container is launched. If I subsequently run docker exec -it [ID] bash, I can get a shell going from inside the container and it successfully executes a conda environment needed for all my python code, so I can just run python script.py and everything runs okay.

I wanted to automate this process for future use, so I wanted to put these commands into a single script so that I don't need to manually type or execute anything from within the environment. The solution I thought would work was this:

docker exec -it [ID] bash -c "python script.py"

but this doesn't work, giving an import error for the python code. My assumption is that the conda environment is not activated, so I try to execute conda activate my-env, which kicks back a new error of:

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.

So, I follow the instructions and run conda init bash first to see if that helps, but this error still kicks back eventually. Ultimately, it seems like if I execute a bash shell first, then manually start running python code everything is fine, but if I try to do it all at once the conda environment cannot be set up for somme reason. Is there a way to make this work without editing the image itself, or is this something that would require rebuilding the image?

Thanks ins advance!

Solution

  • The conda activate function is defined by code added to .bashrc by the conda init command. Bash will not source .bashrc unless the -l (--login) flag is used.

    However, rather than bothering with shell, Conda provides a conda run command that executes within a specified environment. So, try something like

    docker exec -it [ID] conda run -n my-env python script.py

    For interactive scripts, one may also need some of the additional conda run flags, such as --live-stream or --no-capture-output. See conda run -h.