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This page explains how to copy files for your analysis to and from Hydra.

  • File transfers can be done through (Linux/Mac) command line, using scp, rsync or sftp, or
  • using a GUI application like FileZilla, WinSCP or Cyberduck (etc, i.e, any tool that implements the scp or sftp protocol).

  • Transfers to Hydra can only be initiated from "trusted" computers (i.e., you may need to enable VPN);
  • Transfers from Hydra to your local machine are not limited to trusted destinations.

(warning) Files should always be copied directly to the /pool, /data or /scratch directories, not to your home directory (/home) because of space limitations. See (link still missing) about data storage on Hydra.

These quick start instructions show how to configure Cyberduck for file transfers.

Using Cyberduck

 

  1. Download and install Cyberduck. The program is available for Mac and Windows computers.
    Mac screenshots are shown here, but the Windows configuration is similar.
  2. Open the Cyberduck application. 
  3. From the Bookmark menu choose "New Bookmark..."
  4. In the Bookmark menu that opens, set:
    1. Protocol dropdown to SFTP
    2. Nickname to "Hydra"
    3. Server to hydra-login01.si.edu or hydra-login-2.i.edu
    4. Username to your Hydra username
    5. (optional) Under "More Options" set Path to /pool/genomics or another directory you use often. This is the directory that will open when you start the connection.
    6. Close the New Bookmark window to save it 

  5. Open the connection to Hydra by double clicking the bookmark and entering your password when prompted.


    (warning) If you get a warning about an Unknown fingerprint, click the Always checkbox and then the Allow button.
  6. Transfer files to or from Hydra by double clicking in the window to navigate to your fold and then drag and drop files. By default double clicking a file will download a copy to your Downloads folder.
    (thumbs up) You can also use Cyberduck to create directories, delete files, rename files/directories. Use the Action item in the toolbar or right-click to get these options.

    (thumbs up) You can edit text files stored on Hydra using your Mac or PC's text editor by clicking on a text document and choosing "Edit" from the toolbar. You can configure what text editor to use in the Program's preferences.

    Last updated MK/PF/SGK.

 

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