using docker container to execute python script

[tischi]

@BioinfoTongLI

Here the python code is run within the context of the docker container, is it?

Could you explain how one could do the same without Nextflow, just on a CLI?

[BioinfoTongLI]

Hi @tischi， that's correct.
If you want to run it with CLI, just make sure that you're in the your new environment and run with python blur.py --[your-args]
almost the same as in the process.
BTW: if you want to run the the other python scripts, you will need to install fire (the argument parser) with pip install fire

[tischi]

just make sure that you're in the your new environment

Sorry for being such a noob, but how do I do this when using docker? For conda, I know: conda activate ...

[BioinfoTongLI]

you mean in your own docker env? just run the python blur.py part should be fine. If the expected python version is in your PATH

[krokicki]

@tischi Sorry, I just saw this. You can use the Docker container as an environment by mounting your code/data into the container, like this:

docker run -it -v .:/opt bioinfotongli/ome-zarr-nextflow-minimum:latest /opt/bin/blur.py

This assumes you are in your cloned code base (ome-zarr-image-analysis-nextflow) and mounts the current directory as /opt. Then you can access the code as /opt/bin/blur.py. Hope that makes sense.