Transferring Data to/from BMRC

Configuring FileZilla for Two Factor Authentication

FileZilla is a popular tool for SFTP file transfers and can be used to transfer files to/from BMRC with additional configuration as follows.

FileZilla can be downloaded from https://filezilla-project.org/download.php?show_all=1

1. Open FileZilla from the Menu Bar select Edit -> Settings. In the Connection settings tab, set your timeout value to 600 seconds (ten minutes). Then click OK to save your settings.
   
2. From FileZilla's main window, click the Site Manager button (underneath the File menu) to display the Site Manager window.
   
3. Click New Site to configure your connection to the BMRC cluster and copy the details shown above, namely:
   Protocol: SFTP
   Host: cluster2.bmrc.ox.ac.uk
   Port: 22
   Logon Type: Interactive
   User: [Enter your username]
   
   NB If connecting to another BMRC server, adjust the Site Name and Host settings as needed.
4. Now select the Transfer Settings tab, enable Limit number of simultaneous connections and set to 1.
   
5. Now click OK to save this configuration. Back at the main window, click the down-arrow next to the Site Manager button and select BMRC Cluster. This will begin the login process.
6. If FileZilla warns you about an Unknown host key, tick the box marked Always trust this host, add this key to the cache and click OK. (Please contact BMRC if you wish to confirm the key identity further.)
7. FileZilla will now prompt you to enter your First Factor i.e. your password:
   
8. After entering your password and clicking OK, FileZilla will then prompt you to enter your second factor code:
   
9. After entering your second factor code and clicking OK, FileZilla should now be connected. The left hand size of the FileZilla window will be showing files on your local computer. The right hand side will be showing files on the BMRC Cluster (or whatever remote site you have configured). Remember that on the BMRC cluster, all data should be stored in your group area under /well/<group>/users/<username>/ - so you may need to navigate to the appropriate location in the right hand window before dragging and dropping files between the two systems.

Data Transfers Via Globus

BMRC is able to facilitate both incoming and outgoing data transfers via Globus, a popular, secure third party platform for transferring data. Globus is our preferred option when transferring data to/from your research partners who do not have a regular BMRC account, whether they are elsewhere within the University of Oxford or outside the University.

Prerequisites

In order to request a data transfer via Globus, the BMRC user must in the first instance email us with details of the data to be transferred, cc'ing both to their PI for authorisation and to their external collaborator (the intended sender or recipient of the data).

The external collaborator will need :

1) Either: Access to an institutional Globus server. Please ask your institution's IT services whether there is an institutional licence and whether it provides a suitable location for your data to be received or transmitted from.

2) Or: The Globus Connect Personal software installed onto their institutional or personal computer.

Installing Globus Connect Personal

NB Installing Globus Connect Personal is not needed if you are using an institutional Globus account.

To install Globus Connect Personal:

1. Visit the Globus Connect Personal website and download the appropriate client for your operating system. Clients are available for Windows, Mac and Linux. Follow the installation instructions in order to complete the installation.
2. During the installation process, you will be asked to login via the Globus website. You can login with an organisational account, a Google account, an ORCiD ID account or it is possible to create a Globus ID with a username and password. University of Oxford users can now use their SSO to login.
   
3. Once logged in, you will be asked to provide consent to the use of Globus Connect Personal and provide a name for the computer on which you are installing the software. Choose a name that is meaningful to you and click Allow to continue.
   
4. The Globus Connect Personal software on your laptop will now ask you to complete the setup by choosing a name for the data collection on your laptop.
   
   In general, you can use your laptop name as the Collection name. For transfers to/from BMRC, the High Assurance button should be left unticked.
5. Finally, the application should notify you that it has been successfully installed and that the Globus Connect Personal application is now running. Mac and Windows users should find a notification icon in the tray or menubar. Linux users may see a notification icon or the running application window.

Using Globus for Data Transfers To/From BMRC

In order to carry out a data transfer to/from BMRC, you will need to have logged in to an institutional Globus account or configured Globus Connect Personal on your own computer following the steps above. On request, BMRC will enable the ability to create a Globus Guest Collection, which can be shared with external collaborators. Users with regular BMRC cluster accounts will need to request that Globus access is enabled.

Once the above is in place, you can carry out a data transfer by following these steps.

1. Login to the Globus website using the same credentials used previously (whether an institutional login, Google login, ORCiD ID or Globus ID).
2. Once logged in, in the file manager collections search box search for bmrc#upload23. Then click continue to activate the endpoint.
   
3. When activating the endpoint, you will be asked to input the credentials for your BMRC account. You must enter your 2FA code, as this will be enabled for your account, as well as your username and password. You may periodically need to reactivate if you do not use the endpoint.
   
4. The file manager window can be vertically split into two halves by selecting the two-pane view in the "Panels" section in the top right of the webpage . You will see the contents of the BMRC folder and the bmrc#upload23 endpoint on the left side of the screen. You should now search for the collection name you registered for your own computer. If you click in the endpoint search box you will be taken to a new window where you can either search by name or click the Your Collections tab to show your own collections.
   
5. After selecting your collection, you will return to the file manager window, with the BMRC endpoint showing on the left and your own endpoint showing on the right. To transfer files in either direction:
1. Navigate to find the files the need to transfer (either in the BMRC endpoint or your own endpoint).
2. Click the checkbox next to your files or folders to select them for transfer.
3. Click the Transfer & Timer Options button to show advanced options and make sure to select Encrypt Transfer (NB if encryption is not enabled, the transfer will fail, but this should be enabled by default for bmrc#upload23).
4. Finally click the Start button on the appropriate side of the window to begin the transfer.
   
6. Once your transfer has started, you can monitor it from the Activity page (see the menu on the left side of the screen).
7. Once the transfer is in progress, you can logout from the Globus website and the transfer will continue in the background. Please log back in later to confirm that your transfer has completed successfully.
8. In the event that your endpoint activation expires before the transfer has completed, you can simply re-activate the endpoint and the transfer should then automatically resume.