User Guide #2: Download Files Programmatically

In User Guide #1, we downloaded files using the portal’s embedded tools. While straightforward, this method is inefficient for large or numerous files. A better option is programmatic clients, which provide faster downloads and improve reproducibility by tracking data usage.

Programmatic clients include the command line, Python, and R. For faster downloads, the command line and Python clients support multithreading, unlike the R client. All programmatic options allow you to download all data and file annotations with a single command, replacing steps like using the Download Cart.

Refer to the following Synapse documentation articles for guidance:

• Downloading Data Programmatically from a Portal

• Downloading Data Programmatically