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slight modifications
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jkanche committed Dec 13, 2024
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9 changes: 7 additions & 2 deletions README.md
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Expand Up @@ -133,7 +133,8 @@ A minimal manifest file (json) must contain the following fields
- `"python_env"`: A set of commands to activate the Python environment containing this package and its dependencies.

Here’s an example of the manifest file:
```json

```py
manifest = {
"files": your/list/of/files,
"python_env": """
Expand All @@ -154,14 +155,18 @@ which python
}
],
}

import json
json.dump(manifest, open("your/path/to/manifest.json", "w"))
```

For more options, check out the [README](./src/cellarr/slurm/README.md).

- Step 2: Submit the job
Once your manifest file is ready, you can submit the necessary jobs using the `cellarr_build` CLI. Run the following command:

```sh
cellarr_build --input-manifest your/path/to/test_manifest.json --output-dir your/path/to/output --memory-per-job 8 --cpus-per-task 2
cellarr_build --input-manifest your/path/to/manifest.json --output-dir your/path/to/output --memory-per-job 8 --cpus-per-task 2
```

### Query a `CellArrDataset`
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