search

sct-pipeline / binder-example

Example of end-to-end processing pipeline: from Dicom data to MR quantitative results.
MIT License
1 stars 1 forks source link

[NEW] Add Dockerfile #3

Closed mathieuboudreau closed 5 years ago

mathieuboudreau commented 5 years ago

I modified the Dockerfile I was already using for other projects (has SoS, jupyterlkab extensions, plotly, etc), and added the SCT installation to it.

I tested the installation by running a MyBinder instance + JupyterLab (test it out here: https://mybinder.org/v2/gh/mathieuboudreau/binder-example/docker?urlpath=lab), opening a terminal session, and running your pipeline (./batch_processing.sh). Looks like it ran without any issues, this screenshot is from when the script terminated:

capture d ecran 2019-02-07 a 15 15 49

Some fat might be trimmed from the Dockerfile, but some of the addons I've found useful just in case.

This dockerfile is based from a Jupyter one, not an SCT Docker image. I tried to get it working with your SCT Docker image, but I was getting some folder permission issues, as well as the Jupyter session wasn't being setup properly, so instead of debugging that for a while I just decided to start from my Dockerfile that I knew worked for sure.

mathieuboudreau commented 5 years ago

Odd, it worked for me just a minute ago.

Sometimes MyBinder takes longer than other times, which can be frustrating as a user (!). Feel free to try again later to check it.

You'll have to merge, as I don't have permissions in this repo/org.