Add UCE method #7
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Requires more memory than allowed by the local labels config
lazappi
commented
Oct 31, 2024
| rename_keys: 'input_dataset:output_dataset;input_solution:output_solution' | ||
| output_state: "state.yaml" | ||
| publish_dir: "$publish_dir" | ||
| settings: '{"methods_exclude": ["uce"]}' |
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I excluded UCE from the local benchmark scripts because it requires more memory than is allowed by the local labels config
lazappi
commented
Oct 31, 2024
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| # Code has hardcoded paths that only work correctly inside the UCE directory | ||
| if os.path.isdir("UCE"): | ||
| # For executable we can work inside the UCE directory | ||
| os.chdir("UCE") | ||
| else: | ||
| # For Nextflow we need to copy files to the Nextflow working directory | ||
| print(">>> Copying UCE files to local directory...", flush=True) | ||
| import shutil | ||
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| shutil.copytree("/workspace/UCE", ".", dirs_exist_ok=True) |
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This is quite hacky but it was the only way I could get it to work. Happy to hear other suggestions.
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Describe your changes
Adds the Universal Cell Embeddings foundation model as a method
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Proposed changes are described in the CHANGELOG.md
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