Docker #32
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Docker #32
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kaitj
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December 1, 2022 09:31
- Add inputs to rule all for copying freesurfer and zona tsv files to appropriate location
- Adds in rule for labelmerge (needs updating with container and proper command) - Update resources with correct names and paths - Add tsv to rule all for copying from resource to bids folders for labelmerge - Simplify rule all
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Author
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Fixing some workflow bugs that I am going to include in this PR now that I have a working container to push what in theory should be a fully functional containerized workflow. Will mark ready to review once bugs are fixed. |
added 7 commits
December 7, 2022 12:17
Collaborator
Author
|
This workflow was able to run successfully twice now. I am running it one more time to be sure, but should be good for a review |
added 3 commits
December 18, 2022 13:08
- instead of running over each participant in the dbsc rule, expand over all inputs and outputs (labelmerge will run once for all subjects)
added 2 commits
December 27, 2022 16:21
- Flag to indicate use of SLURM_TMPDIR, else use /tmp - SLURM_TMPDIR is passed via os.environ.get
- uses Path.parent to avoid creating a nested subject directory within desired output directory
tkkuehn
approved these changes
Jan 10, 2023
Contributor
|
Just going to wait for #35 before merging this. |
added 3 commits
January 18, 2023 10:36
- if include_subject_dir=True, subject appears twice in the dir path
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Proposed changes
This PR resolves #23. Adds a container build with required dependencies (based on the
labelmergebranch).For v0.2.x, should also look into running directly from the container. Would likely need something similar to how
hippunfoldhandles running the workflow from within a container.Types of changes
What types of changes does your code introduce? Put an
xin the boxes that applyChecklist
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xin the boxes that apply. You can also fill these out after creating the PR. If you are unsure about any of the choices, don't hesitate to ask!poe qualitytaskNotes
All PRs will undergo the unit testing before being reviewed. You may be requested to explain or make additional changes before the PR is accepted.