To perform a bulk export of data, you will need to send the files from the INCLUDE Data Hub to a CAVATICA project using the Data Exploration – Data Files Tab.
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.
Bulk Download of Files Using the CAVATICA API
- 1. Install the Seven Bridges Command Line Interface
Open your terminal application, then execute the following:Shell
curl <https://igor.sbgenomics.com/downloads/sb/install.sh> -sSf | sudosh- 2. 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.
- 3. Configure the Seven Bridges Command Line Interface
In your terminal application, execute:Shell
sb configureThe 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
- 4. Generate a list of files you want to download
In your terminal application, execute:Shell
sb files list --project your-username/project-name > filelist.txt- 5. Download the Files
In your terminal application, execute:Shell
cat filelist.txt | cut-d"'"-f2 | xargs -I % sb download --file %Your files will begin downloading now.
