Bind files/directories into containers?

[effigies]

It seems the command for running containers is in https://github.com/ReproNim/containers/blob/master/.datalad/config

Is there a way to add arguments like -B /my/patch:/patched/location?

Not sure if this belongs in reproman...

[yarikoptic]

It seems the command for running containers is in https://github.com/ReproNim/containers/blob/master/.datalad/config

correct!

Is there a way to add arguments like -B /my/patch:/patched/location?

yes -- modify that file or if for some reason you need to apply it systematically for all containers -- https://github.com/ReproNim/containers/blob/master/scripts/singularity_cmd#L104 itself.

If config file -- then better make use of recently added in #88 functionality to "copy" definition into corresponding super-dataset, and adjust there. That usage already presented in https://github.com/ReproNim/containers#runnable-script and adjusted details docs are coming (#90 attn @asmacdo).

But could you tell me more about your use case?

Note that binding of "external" to dataset paths is generally "ill-advised" since would violate YODA principles. That is why the https://github.com/ReproNim/containers/blob/master/scripts/singularity_cmd binds everything only under current dataset.

Not sure if this belongs in reproman...

who knows... it might ;)

[effigies]

We have a weird bug where SVD is failing on an image affine in an MRIQC run, but I can't reproduce it locally. I want to just patch the nibabel module to catch the exception and provide a more informative error (what was the affine that failed?) without going through the process of making a release or otherwise building a custom image. The idea would be to include the patched file inside <dataset>/code/ so it would be reproducible if weird.

[yarikoptic]

So why don't you start with that target - placing patched code under <dataset>/code which should be visible under that path within the container?

[effigies]

Hmm. I suppose I could put a whole patched nibabel in and add it to PYTHONPATH.

[yarikoptic]

you could. Also don't forget about possibility for submodules so you could just have just a patched branch of the nibabel