Links

dbGaP Data Transfers

The DbGap xfer server is available to import and export data for DbGaP-based projects. Group membership is required for users to log in dbg_import, dbg_export. Connectivity to the xfer server is restricted to Brown networks, remote users will need to first log into the F5 VPN for access. Instructions for downloading new datasets and exporting results are not similar and require different client software.

Downloading new datasets

​
​
  • Start FastX on your local workstation.
  • Click the “+” icon to create a new entry.
  • Select “SSH”.
​
​
  • Enter the connection details:
Host: pdbgxfercit.services.brown.edu
Port: 2223
User: <your Brown username>
  • Click Save.
​
​
  • You will be prompted for your password, enter it, and click Continue.
​
​
  • You will be prompted to select a Duo authentication method. Enter the number of your choice and click Continue. Confirm your Duo authentication in the manner you selected.
​
​
  • After logging in, click the “+” icon to launch a FastX application.
​
​
  • Select Desktop and click OK.
​
​
  • A Linux Desktop session will launch (this can take several seconds). The Aspera Connect client will be silently installed for your account.
  • Open a web browser or terminal session to download the necessary client software if required.
​
​
  • Data sets need to be saved inside the import area to be usable on Oscar.
  • The import area can be accessed from a folder on your desktop, or in ~/import/.
  • In the import area, you can save to your user folder or to any project folder you may have access to.
​
​

Exporting results data

​
​
  • Start Filezilla on your local workstation
  • Click File > Site Manager
  • Enter the connection details:
Protocol: SFTP - SSH File Transfer Protocol
Port: 22 (or leave blank)
Host: pdbgxfercit.services.brown.edu
Logon Type: Interactive
User: <your Brown username>
  • Click Connect to begin the login process.
​
​
  • Accept the server’s host key by clicking OK.
​
​
  • You will be prompted for your password, enter it and click OK.
​
​
  • You will be prompted to select a Duo authentication method. Enter the number of your choice and click Continue. Confirm your Duo authentication in the manner you selected.
​
​
  • On the Remote site (right) pane, double-click the Results directory.
  • Drag file(s) from the Remote site to your Local filesystem (left) pane.
​
​