To perform a bulk export of data, you will need to send the files from the Kids First Portal to a Cavatica project using the File Repository Tool.
Once your files are in a Cavatica project, the recommended course for downloading is to use the Seven Bridges Command Line Interface to download the files.
Install the Seven Bridges Command Line Interface:
Open your terminal application, then execute the following:
curl <https://igor.sbgenomics.com/downloads/sb/install.sh> -sSf | sudo sh
Get your Authentication Token
Go to Cavatica. After logging in, click the Developer tab at the top of the page and then click Authentication Token in the drop down. On the page, click on Auth Token. Your authentication token is on this page.
Configure the Seven Bridges Command Line Interface:
In your terminal application, execute:
sb configure
The interface will ask for the Authentication Token you found in the previous step and the API endpoint. The API Endpoint is: https://cavatica-api.sbgenomics.com/v2
Generate a list of files you want to download:
In your terminal application, execute:
sb files list --project your-username/project-name > filelist.txt
Download the Files:
In your terminal application, execute:
cat filelist.txt | cut -d "'" -f 2 | xargs -I % sb download --file %
Your files will begin downloading now.