/download_pyega

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How to download datasets from pyEGA

Requirements

In order to download datasets from pyEGA, several requirements must be met:

  1. Access granted to the dataset.
  2. A valid EGA account. (username and password)

The EGA account credentials must be inserted in the credentials.json file:

```json
{
    "username": "your_username",
    "password": "your_password"
}
```

  1. A pyega3 client installed.

    # with pip
pip install pyega3

# with conda
conda install -c bioconda pyega3

  2. The dataset accession number. This can be found in the EGA dataset page.

Downloading datasets

Once the requirements are met, the datasets can be downloaded using the download.sh script. Ideally, this would be run as a SLURM job, but due to the amount of data to be downloaded, this must be run in the /dipc/ partition.

In order to run the script, fill in the requested information (credentials' file path, dataset accession number) and run the following command:

nohup bash download.sh &

The script will download the dataset to the /dipc/ partition, in the current working directory.

To check the download progress, run the following command:

tail -f nohup.out