Provide neurodesk convenience command

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#113 opened on Apr 18, 2024 0 comments 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty: 5/5
Estimated time: Over a week
Newbie friendliness: 20/100

Issue type: Feature
Clarity: Needs clarification
Activity status: Stale
Tech stack: python
Domain: cli

Research direction

Start by reading transparent-singularity/run_transparent_singularity.sh and ts_binaryFinder.sh, along with the neurocontainers afni/build.sh entry-point generation. Then review how lmod-loaded environments and the proposed datalad neurodesk-run TOOL command could be represented. Done would require a defined lookup across the loaded stack and a commit message identifying the used container.

Written by the indexing model from the issue text.

Description

neurodesk uses lmod to provide entry points (tools) for each container
- currently there is no centralized/recorded manifest. container has BIN path pointed to https://github.com/NeuroDesk/neurocontainers/blob/master/recipes/afni/build.sh#L34C4-L34C41 and upon build script generates all lmod entry points.
  - https://github.com/NeuroDesk/transparent-singularity/blob/master/run_transparent_singularity.sh#L212 runs
  - https://github.com/NeuroDesk/transparent-singularity/blob/master/ts_binaryFinder.sh
- considering adopting singularity-hpc (shpc, https://singularity-hpc.readthedocs.io/)
- NB: somewhat relates to the effort @yarikoptic tried to do somewhere to create index of all files per each container
lmod could load multiple container "environments" (with version) so that later loaded container entry points take precedence over earlier
what if we could do smth like datalad neurodesk-run TOOL which would then "lookup" within currently loaded "stack" of environment which actual container and which tool gets invoked and then the datalad would have a commit message pointing to that particular used container (within repronim/containers collection)

attn @stebo85

Dominant language: Python
Stars: 32
Forks: 17
Avg merge: 12h 2m
Merged PRs (30d): 3

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