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khanlab / tar2bids

GNU General Public License v3.0
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Revamp dockerfile #28

Closed tkkuehn closed 2 years ago

tkkuehn commented 2 years ago

This adjusts the Dockerfile to make it a bit simpler (while retaining version flexibility) and use a more recent container base (Debian Bullseye). It no longer uses conda or NeuroDebian, instead using precompiled binaries and/or Debian Bullseye repositories. It now:

  1. Installs dcm2niix from the compiled binaries provided in their GitHub releases.
  2. Installs heudiconv with pip.
  3. Installs the BIDS validator from npm.
  4. Installs GNU parallel from the Debian repos.
  5. Installs flirt and fslorient from the Dropbox link (same as the old Dockerfile).
  6. Installs pydeface from GitHub (same process as the old Dockerfile).

Created as a draft because CircleCI fails to build the container even though it built locally for me (I think CircleCI would need to use a more recent version of Docker). I'll try to get a GitHub action to build it set up then move it out of draft status.

In the meantime, I'm happy to make adjustments to this approach if there's anything I'm missing.

tkkuehn commented 2 years ago

Okay, I think this is ready to go. @akhanf before we can merge this we'll want to add DOCKER_USERNAME, DOCKER_PASSWORD, and GITHUB_TOKEN to this repo's secrets and disable the CircleCI build.

akhanf commented 2 years ago

thanks! I've added those secrets, and removed circleci, so looks like this can be merged in now!

tkkuehn commented 2 years ago

Great, I'll merge this and keep an eye on the Docker push action next time there's a release (not sure if that's automatic).