Single Cell Expression Atlas Knowledge Graph

Installing Dependencies

This project uses Poetry to manage dependencies. If you haven't installed Poetry yet, you can do so by following the instructions on the official Poetry website.

Once you have Poetry installed, you can install the project dependencies by navigating to the project directory in your terminal and running the following command:

poetry install

This command will read the pyproject.toml file and install all the dependencies listed there.

Running the bulk experiments script with Poetry

You can run the bulk_experiments.py script from the command line. Here's an example of how to do it:

poetry run python src/bulk_experiments.py --study_filter <study_filter> --chunk_size <chunk_size> --download

Replace <study_filter>, <chunk_size>, and with the appropriate values.

• study_filter: A string to filter specific studies.
• chunk_size: An integer indicating the number of studies to process at a time.
• download: (Optional) A boolean flag indicating whether to download files. Pass it to download files and omit it otherwise.

For example, to process studies that contain the word "E-CURD" in chunks of 10 and download the files, you would run:

poetry run python src/bulk_experiments.py --study_filter E-CURD --chunk_size 10 --download