Update singularity image locations for sumner2 #87
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bergsalex
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SkepticRaven,
gbeane,
jacobbeierle,
keithshep and
michberger
michberger
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michberger
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Just a question...why are there multiple latest.sif in each of the images? Some are in a folder called "latest" and some inside a version folder. There is probably a logical reason but it strikes me as redundant files.
| container = "/projects/kumar-lab/meta/images/mouse-tracking-runtime/RBase/v0.1.2/latest.sif" | ||
| } | ||
| withLabel: "gait" { | ||
| container = "/projects/kumar-lab/multimouse-pipeline/nextflow-containers/gait-pipeline-2025-03-27.sif" |
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Gait is a difficult one to version right now. It has unrelated histories between private (bitbucket) and public (github, cited paper version). I think the differences are just in Gautam's analysis and vms.
It looks like the paper version is v1.0.0.
The runtime currently there should probably be v1.1.0.
| container = "/projects/kumar-lab/multimouse-pipeline/nextflow-containers/gait-pipeline-2025-03-27.sif" | ||
| } | ||
| withLabel: "frailty" { | ||
| container = "/projects/kumar-lab/multimouse-pipeline/nextflow-containers/vfi-2025-03-27.sif" |
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VFI paper version was v1.
There should probably be a new release based on the history. Recommend v1.0.1 (all look like bugpatches).
| container = "/projects/kumar-lab/multimouse-pipeline/nextflow-containers/sleap-io-0.2.0.sif" | ||
| container = "/projects/kumar-lab/meta/images/mouse-tracking-runtime/sleap-io-0.2.0/v0.1.2/latest.sif" | ||
| } | ||
| withLabel: "rclone" { |
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rclone container is a trivial container definition. I only add bash to the container so that nextflow logging can run. The version it's running happens to be rclone v1.70.3 (according to the tool itself).
I can add the definition file to the vm folder in this PR if you want.
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That would be great.
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Added vm/rclone.def
Feel free to be more specific about its version, but I don't think it matters much.
All of the For example:
We should probably have a lab wide presentation on the new image and classifier directory structures. |
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I'm going to merge as is for now so that @michberger can use the updated images. I'll make a new PR once we have final paths for the remaining images. |
This PR updates the singularity image locations to reference the new meta/images image repository.
Before we merge this, I would like to check with @SkepticRaven about the
gaitfrailtyandrcloneimages.