Using Globus

Globus is a data transfer tool which facilitates the scheduled high-speed transfer of large amounts of data between research organisations, or between research organisations and users' personal devices.
There is a BEAR Globus endpoint that connects directly to the Research Data Store (RDS) storage facility.

Access to Globus is via the Globus Web App. The Globus-CLI (command line tools) are also available on BlueBEAR login nodes.

In addition to the University of Birmingham endpoint, Globus is used by several large international scientific organisations including ORNL, CERN, Sanger Institute, Crick Institute, and ARCHER (UK Research Data Facility).

For personal devices, for example laptops, you can use Globus Connect Personal to transfer data quickly to and from the Research Data Store.

How Globus works

When transferring data using Globus:

1. The transfer is scheduled via the web interface.
2. The transfer happens directly between two Globus endpoints (technically using Globus Data Transfer Nodes, or DTNs) in the background.
3. The use of parallel streams makes the transfer significantly faster.
4. The transfer continues even if you close your browser.
5. You receive an email notification when transfers complete, or if there are any errors.

Logging in to Globus

The login process uses the University of Birmingham's single sign-on (SSO) service, connected to Globus via a broker called CILogon. When you first use Globus, follow the prompts to create a Globus account and link it your University account.

To access Globus, browse to Globus Web App.

First time login steps

1. Navigate to the Globus Web App:

   

2. Search for "University of Birmingham" in the "Look-up your organisation" box:

   Warning

   Please ensure that you select "University of Birmingham" and NOT "University of Birmingham Development IDP".

   

3. Globus uses federated authentication via CILogon. Click "Continue" to be redirected to the University's SSO web page:

   

4. Use your normal University credentials to authenticate. You will then be redirected back to the Globus website:

   

   If you have previously used Globus at another organization, you can "Link to an existing account". Otherwise, click the "Continue" button.

5. Confirm you are happy for your email address to be passed to Globus to create an account:

   

   You can opt in to receive Globus email updates if you want.

6. Once you click continue, you will see:

   

   Click "Allow" to grant the necessary permissions to Globus.

Once you have logged in for the first time, you won't need to link your account again.
For convenience, the web browser remembers your preferred organisation to speed up future logins.

Accessing the BEAR Globus endpoint

To transfer data to or from Research Data Store storage, you need to connect to the "University of Birmingham BEAR" endpoint.

1. Once logged into Globus, select the "File Manager" icon:

   

2. In the "Collection" box, start searching for bear:

   

   Click on "University of Birmingham BEAR" to automatically connect to the BEAR Globus endpoint.

3. By default you start in your BlueBEAR home directory (this may be empty if you are only a user of RDS storage):

   

To access other parts of the storage, type the path to your RDS folder in the "Path" box, e.g., /rds/projects/2015/XXX. Note that this is the "BEAR Linux path" rather than the path you might use on Windows or macOS.

For information on locating the BEAR Linux path for a given project, see Connecting to the RDS via Linux.

Transferring data on BEAR using Globus

When you transfer data using the Globus web app, this is a scheduled data transfer that happens in the background. You can transfer data both from and to the BEAR Globus endpoint.

1. To start a data transfer, select the File Manager in the Globus web app and connect to the BEAR Globus endpoint. To the right of the window, you should see a "Transfer or Sync to..." link. When you click this, the window should split:

   

2. Click the "Transfer or sync to..." box on the right to select another Globus endpoint. Search for the Globus endpoint you want to transfer data from or to in the "Collection" box. Note that the endpoint can be a personal device if you've set up Globus Connect Personal.

   In the following example, we are using the "Shared EMBL-EBI public endpoint" for testing:

   

   Note

   The "Shared EMBL-EBI public endpoint" is read-only, meaning you can only transfer data from it to the BEAR Globus endpoint.

   Select the file(s) you want to transfer either from Birmingham (left) or to Birmingham (right). Hold the CTRL key to select multiple files.
   Click the "Start" button under the appropriate column (i.e. depending on transfer direction) to schedule the data transfer.

3. Check on the progress of the transfer by selecting "Activity" on the left-hand toolbar. Depending on your account settings, you may also receive an email once the data transfer has completed:

   

Endpoint Credentials

When accessing some Globus endpoints, you may need to use local credentials. For example, if you are transferring data from Diamond Light Source, you may be asked to enter your Diamond Light Source username and password:

Sharing data with external users

Globus allows you to share directories with external users without them needing a University account. This sharing facility is enabled on the BEAR Globus endpoint.

Sharing Permissions

When you share a folder with an external partner, they inherit your access permissions for the entire folder tree and will be able to read any file you can access. We therefore strongly recommend that you don't share the "top" of your storage folder but create a folder specifically for sharing.

Setting up a share

For detailed instructions on setting up shares, follow the Globus documentation: How To Share Data Using Globus

First-Time Globus Users

If the person you are sharing data with has never used Globus before, we recommend that you ask them to login to Globus first. Whilst they may receive the sharing email from Globus, they may get "Access Denied" errors to the folder after login due to the way identities sometimes appear to Globus.

If this happens, once your collaborator has logged into a Globus account, you need to edit the permissions on the share. Enter the email address in the box and click "Search" rather than "Add". This should then find the Globus account and grant access to the collaborator.

Instructions for external (non-UoB) users

External collaborators who have been granted access to a shared folder should follow these instructions:

Downloading files from a shared folder

1. You will receive an email invitation similar to this:

   

   Use the URL in the email to access the folder (copy and paste it into your browser). The link will direct you to authenticate yourself.

2. You will be taken to a login page:

   

3. Login using your Globus ID credentials (or create a new account if this is your first time using Globus):

   

4. You will see the File Manager view showing the shared folder:

   

5. Click on the shared folder to reveal any subfolders within it:

   

6. Select the file or folder you want to download and click on "Transfer":

   

7. On the right-hand side, click "Search" to locate the endpoint (your computer) you want to transfer the data to:

   

   Note

   You will need to have Globus Connect Personal installed on your computer to create a personal endpoint.

8. Select your endpoint and then the folder on your computer where you wish to download the data:

   

9. Press the "Start" button to initiate the download. You will see a confirmation pop-up:

   

   If you click "View details", you will see the transfer progress:

   

   The data transfer will take time depending on how much data is being transferred.

10. Check the destination directory for the files:

    

    You will also receive an email confirming that the data has been copied.

Uploading data to a shared folder

To upload data to a shared folder:

1. Select the Globus Connect Personal endpoint on your device (where your data is located) and navigate to the relevant folder path.

2. Select the files or folders you want to transfer and click "Start":

   

3. You should see a confirmation pop-up:

   

4. Click the refresh button at the top of the page to check the transfer status. You will receive an email when the upload has been successful:

   

Further information

• Generic Globus documentation: https://docs.globus.org
• How to share data: How To Share Data Using Globus
• Back to: BEAR Data Transfer Guide

Further Assistance

If you need further help, please raise an Other BEAR Request ticket on the Service Desk.

If you need to report a fault with the service, please raise a Report a Fault with BEAR ticket on the Service Desk.