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mathesong / bloodstream

A PET BIDS blood-processing tool
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Update docker support #12

Closed mnoergaard closed 1 year ago

mnoergaard commented 1 year ago

This PR suggests an alternative way to run bloodstream in a docker container. It simplifies the execution by asking the user to create a single config.json file and add it to the /path/bids/code/bloodstream, including an extra R analysis script (run_bloodstream.R) that also should be added to this path. After this, bloodstream can easily be run using docker.

Documentation has also been updated to match the workflow, and one is (for now) supposed to build the docker container themselves. In the future, this should ideally be pushed to docker hub.

mnoergaard commented 1 year ago

@mathesong: updated the docker file to now create the R script inside the container.

mathesong commented 1 year ago

Sweet!! That makes everything so frictionless! Love it! I'll merge directly.

mathesong commented 12 months ago

By the way, based on your PR, I've updated the docker support a little bit. Just so you don't freak out if/when it stops working the next time you update.

It's a bit more flexible now: now it can run without a config file at all, and it will just perform linear interpolation. And if you want to use a config file, then it no longer needs to be called config.json: the config filename can just be specified as an input argument to docker run.

mnoergaard commented 11 months ago

Awesome @mathesong - looks good!