Tree Of Life 200M tools, configurations, documentaion#25
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Andrey170170 merged 16 commits intomainfrom May 22, 2025
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Updated configuration files to support excluded servers and added support for additional download settings. Introduced new README guides for FathomNet, BIOSCAN, and Safe download workflows, ensuring clear postprocessing instructions. Included detailed Slurm script documentation for tool submission and management.
Introduce a new configuration file, `eol_download_config.yaml`, for managing Encyclopedia of Life (EoL) downloads within the Tree of Life 200M dataset. Also, add a detailed `EoL_download_README.md` documenting the step-by-step process for downloading and post-processing the data. Removed "eol" from `safe_download_config.yaml` to separate download workflows.
Introduce a new `tol200m_fathom_net_crop` module that processes and crops images based on bounding box metadata. It includes components for filtering valid image partitions, scheduling distributed tasks, and performing cropping operations with updated metadata. Added a comprehensive README detailing the tool's functionality, configuration, and pre/post-conditioning requirements.
…eduler Introduce `tol200m_bioscan_data_transfer` module, including classes for data transfer, scheduling, and processing with MPI. Updated README with configuration details for the new module and added imports to the main TreeOfLife toolbox.
Revised and improved download guides for BIOSCAN, GBIF, FathomNet, and EoL, including clearer component-specific details, troubleshooting, and updated configurations. Central README updated to reflect new structure and improved guidance for TreeOfLife200M dataset setup.
Updated README files for both new tools.
…cesses - Introduced bioscan_download_config.yaml with detailed parameters for BIOSCAN dataset. - Updated eol_download_config.yaml, fathomNet_download_config.yaml, general_download_config.yaml, and safe_download_config.yaml to include destination folders for images and errors. - Enhanced README files for BIOSCAN, EoL, FathomNet, GBIF fast, and GBIF slow downloads to reference new config files and provide clearer instructions.
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Some questions, likely relevant to the other configs
| path_to_input: "path_to_input_file" # Path to the input file with the list of servers | ||
| path_to_output_folder: "path_to_output_folder" # Path to the output folder | ||
| provenance_path: "" # Path to a provenance Parquet file containing source metadata | ||
| path_to_tol_folder: "" # Path to where you save TOL data folder (a.k.a. `<output_dir>/data`) |
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Where you want to save it or where it has been saved?
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| account: "account_name" # Account name for the cluster | |||
| path_to_input: "path_to_input_file" # Path to the input file with the list of servers | |||
| path_to_output_folder: "path_to_output_folder" # Path to the output folder | |||
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What goes to this output folder?
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For bioscan specifically, only partitioned metadata, the images are transferred directly to the ToL save location
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| scripts: | ||
| # Wrapper scripts to submit jobs to the cluster | ||
| general_submitter: "path_to_general_submitter_script.sh" |
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These should probably be e.g., "path/to/general_submitter_script.sh"
Co-authored-by: Elizabeth Campolongo <38985481+egrace479@users.noreply.github.com>
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Comments on Docs (mostly updates to phrasing and adding links to sources)
| ### 1. Setup and Download | ||
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| 1. **Install and Configure Downloader** | ||
| - Set up the `distributed-downloader` package following the [official instructions](https://github.com/Imageomics/distributed-downloader/blob/9ef8b0d297f7a868fac31b2b9c3d5f3aa5533472/docs/scripts_README.md) |
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This should be pip installable or it's about where the scripts are located?
egrace479
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Co-authored-by: Elizabeth Campolongo <38985481+egrace479@users.noreply.github.com>
Added installation instructions
egrace479
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May 22, 2025
Co-authored-by: Elizabeth Campolongo <38985481+egrace479@users.noreply.github.com>
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May 22, 2025
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