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Missing requirements in docker container for spike sorting with kilosort3 #3540

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steevelaquitaine opened this issue Nov 15, 2024 · 0 comments
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extractors Related to extractors module

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@steevelaquitaine
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steevelaquitaine commented Nov 15, 2024

Two requirements are missing to run kilosort3 container "remfile" and "pynwb"-

e.g., The code below produces ModuleNotFoundError for these two dependencies:

# spike sort with kilosort 3 from container (uses apptainer)
sorting_KS3 = ss.run_sorter(sorter_name="kilosort3", singularity_image=True, recording=recording)

Currently the container runs successfully by adding the extra_requirements argument:

# spike sort with kilosort 3 from container (uses apptainer)
sorting_KS3 = ss.run_sorter(sorter_name="kilosort3", singularity_image=True, recording=recording, extra_requirements=["remfile","pynwb"])
@alejoe91 alejoe91 added the extractors Related to extractors module label Nov 15, 2024
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Labels
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