Kids First CAVATICA Python Tools Repository

Requires

Python >= 3.6

Installation

pip install git+https://github.com/kids-first/kf-cavatica-python-tools.git

Setup

To authenticate with sevenbridges, this package looks for a sevenbridges credential profile. For instructions to set up a credential file, see instructions on Sevenbridges' website, here.

Make sure to set the endpoint to the cavatica api endpoint https://cavatica-api.sbgenomics.com/v2in the config file.

Recipes

Download files from a Cavatica Project

In the recipes directory in this repo is a script to download files. Pass that script the name of the project you want to download all the files from and the location you want to save the files.

Download All the Files in a Cavatica Project

To run the script from your shell:

python recipes/download_files.py --project project_name  --download_location path/to/files

Download Files from a Directory in a Cavatic Project

To only download files in a specific directory in a project, specify the path to those files within the project

To run the script from your shell:

python recipes/download_files.py --project project_name  --download_location path/to/files --project_path path/to/stuff

Notes

If a file can't be downloaded, a warning is sent to the console. Archived files can not be downloaded from the API. To Download archived files, they first need to be restored in Cavatica.