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cunningham-lab / neurocaas_contrib

Repo to help develop on AMIs associated with NeuroCAAS
GNU General Public License v3.0
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Add all script files for YASS and BehaveNet analyses on NeuroCAAS. #24

Closed johnlyzhou closed 3 years ago

johnlyzhou commented 3 years ago

The YASS (Yet Another Spike Sorter) and BehaveNet analyses require multiple dataset files with flexible extensions and names. In addition, they offer certain optional commands (or have other environment setup requirements) that require user input and cannot be done in an automated NeuroCAAS analysis.

The current NeuroCAAS drag-n-drop interface only allows for a single dataset file for each analysis (selecting multiple dataset files launches a separate analysis instance for each file). However, all uploaded dataset files are available in the S3 bucket.

Use the config file to provide all filenames required for the analysis and analysis options, and upload those files as dataset files. Call Python scripts through the internal bash script to parse config file, download all specified dataset files, and run any desired optional commands. Since the config file specifies dataset filenames, selection of a dataset file in the NeuroCAAS web interface does not matter (can just choose any one).

cellistigs commented 3 years ago

Thanks John! Running tests now.

cellistigs commented 3 years ago

Tests are failing because John is an outside collaborator and we depend on docker. I've examined the files manually, and they look good to go.