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DATA STORE USER MANUAL
UPCOMING MAINTENANCE

CyVerse systems will be unavailable, as follows:

Access to ALL CyVerse systems will be impacted during network equipment upgrades of core network equipment upgrades from Sunday, May 28 at 12 Midnight to Monday, May 29 at 8:00 AM (check your local timezone here).

CyVerse will perform regular maintenance on key systems on Tuesday, May 30 from 8 AM to 4 PM MST. Access to or usage of the following services will be unavailable or disrupted:

  • Discovery Environment: Currently running analyses will be terminated. Please plan accordingly.
  • Data Store: Unavailable during the maintenance period.
  • Atmosphere: Atmosphere instances will continue to run, but access to instances or to the web interface will be unavailable.
  • Agave/Science API: Unavailable during the maintenance period.
  • CyVerse User Portal: Unavailable during the maintenance period.

Please contact suppport@cyverse.org for any questions or concerns.

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About Cyberduck for bulk transfers for Mac OS and Windows

Cyberduck is a free cross-platform, high-throughput and parallel data transfer open source file transfer program that supports multiple transfer protocols (FTP, SFTP, WebDAV, Cloud files, Amazon S3, etc.). It serves as an alternative to the iDrop Java applet, and has been extensively tested with large data transfers (60-70 GB) from desktop to the CyVerse Data Store. This allows users to transfer large files, depending on the user's available bandwidth and network settings.

What browsers can I use?

Cyberduck versions are available for Mac OS (10.6 and higher on Intel 64-bit) and Windows (Windows XP, Windows Vista, Windows 7, or Windows 8). LINUX users should use iDrop Desktop or iCommands. Cyberduck version 4.7.1 (released July 7, 2015) and later supports the iRODS protocol.

Do I have to have an account?

You must have a CyVerse account to upload files and directories to the CyVerse Data Store, but an account is not required to download files using Cyberduck that have been made available for public use in Data Commons. CyVerse account users can download all community data, as well as upload files and directories to the Data Store.

Want to learn about other upload and download methods?

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 For information on the other upload and download methods, see Downloading and Uploading Data.

Installing and configuring Cyberduck

Step 1: Install or update Cyberduck 

  • If Cyberduck is already installed, check if you need to update (this allows you to be compatible with iRODS 4.1.9):
    1. Click the Cyberduck menu.
    2. Click Check for Updates.
    3. Determine if your installed version requires an update:
      • If using < 4.7.0, the update is required.
      • If using > 4.7.0 and < 5.0.0, the update is recommended.
      • If using 5.0.0 and later, the update is optional.
    4. Depending on your version, click Install Update.
  • To install Cyberduck for your operating system for the first time:
    1. Go to the Cyberduck installation page at https://cyberduck.io/ .
    2. Follow the steps for your OS (not available for LINUX users):
      • For Mac OS:
        1. Click Download Cyberduck for Mac.
        2. Move the downloaded file (either a zip file or the unzipped application file, depending on your browser) to your Applications folder.
          If the zip file is listed, unzip the file in your Applications folder.
          IMPORTANT: The file must be located in your Applications folder.
      • For Windows:
        1. Click Download Cyberduck for Windows.
        2. Locate the downloaded file and double-click to begin installation.
        3. Go through the install process.

Step 2: Configure Cyberduck for use with the Data Store (one-time only)

These instructions are for configuring the iRODS Connective Profile for the Data Store, both for CyVerse user account access and for anonymous access, if you do not have a CyVerse user account.

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This configuration is for the CyVerse main Data Store. To connect Cyberduck to a federated or dedicated resource server, please contact your network administrator.

  1. Click  Cyberduck app icon to open Cyberduck.
  2. Click this link to download the Connection Profile, which contains preconfigured settings for using Cyberduck with the CyVerse Data Store.
  3. Click to open the downloaded iPlant Data Store.cyberduckprofile file.

     Example

  4. Verify iPlant Data Store is displayed in the first field.
  5. In the Nickname field, enter data.cyverse.org – iRODS.
  6. Create the connection:
    • In the Server field, verify that it shows data.iplantcollaborative.org.
    • In the Port field, enter 1247.
    • To create the connection with your CyVerse user account for login:
      1. Enter your CyVerse user name in the Username field.
      • Verify your username is added to the URL field, as shown above.
        Example: irods://yourusername@data.iplantcollaborative.org.
    • To create an anonymous connection so you can access public data without a CyVerse user account:
      1. Click the Anonymous Login checkbox.
      2. Verify anonymous is displayed in the Username field.

The remaining fields are populated.

7. Click in the Transfer Files drop-down list and select Open multiple connections.

8. Close the window.

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For information on configuring your Cyberduck preferences, see the Cyberduck Preferences Help page on the Cyberduck website.

Using Cyberduck

About these steps

These instructions give you the main steps for downloading and uploading files to the CyVerse Data Store using Cyberduck.
For more information on how to use Cyberduck, please see the Cyberduck Help manual, the Cyberduck FAQs, or contact Cyberduck Support.

Logging In

  1. If necessary, click    to open Cyberduck.
  2. In the Cyberduck window, click the bookmark to use and then click Open Connection.
  3. In the drop-down list, click the repository to use.
  4. Log in to Cyberduck:
    • If logging in with your CyVerse account, enter your CyVerse username and password.
    • If logging in without a CyVerse account, click the Anonymous Login checkbox.
  5. Click Connect.

Downloading a file or folder from the Data Store (CyVerse users and anonymous users)

  1. Click the file or folder to download.
  2. Click the Cyberduck File menu and then click New Download. The file is downloaded to your default download folder.
    • To change your default download folder, click , click Download Folder and select the new default download folder.
  3. To navigate to a different folder (for example, to download a file from the Community Data folder):

    Do not click iplant/home or iplant/

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    Clicking iplant/home or iplant/ will cause your system to hang.

    1. Click the Cyberduck Go menu and then click Go to Folder:

    2. Enter the path to the folder (you may want to copy the path to the folder displayed in the DE Data window's Viewing field).
      For example, to go to the Data Store Shared folder, enter /iplant/home/shared, as shown above.
    3. Click Go.

Uploading a file or folder to the Data Store (CyVerse users only)

 Want to sign up for a CyVerse account?

See Create Account on the CyVerse website.

  1. Click the Cyberduck File menu and then click Upload
  2. Click the file or folder to upload and then click Upload.
    The item is uploaded to your Home folder.

Need help?

For assistance installing and configuring Cyberduck for use with the Data Store, please contact CyVerse Support, or see the Cyberduck Preferences Help page for more information on installation.

For questions on using Cyberduck, please see the Cyberduck Help manual, the Cyberduck FAQs, or contact Cyberduck Support.