If you find an error in any of these pages or there's information which isn't provided that you feel would be useful, please contact us via the address provided below. Our documentation is important to us and we treat errors and omissions as problems to be fixed.
- Modern Python versions with hundreds of packages pre-installed
- Modern R versions with over 1000 libraries preinstalled
- A high performance compute cluster
- All major bioinformatics databases
There are two different ways to connect to the CCB servers. For a full graphical login you can use X2Go ; this remote desktop software allows you to connect to a server and run graphical applications, giving a familiar ‘desktop view’ with pull down menus, desktop icons and file browser window options. For fast command line access, you can also connect using any SSH client ; both tmux(1) and screen(1) are installed for session persistence between logins. If you don't need to run a graphical application, such as R-Studio, we recommend taking some time to get comfortable using plain SSH. It's quicker over slow internet connections, avoids keyboard mapping issues and works more reliably.
Please note that CPU and memory resources on the login nodes are not unlimited and that there are watchdog programs which ensure that a single user account can't monopolise them or cause the system to become unstable. See cpuwatch(7) and memwatch(7) for further details.
$ passwd
- your password must be at least 16 characters
- it must not be a password used anywhere else
- you must never, ever share it
For more information on choosing secure passwords, please see the University's Information Security website at https://www.infosec.ox.ac.uk/create-strong-passwords
If you're confident that you know exactly what you're doing you are, of course, free to modify this in any way you wish. At the same time, please be aware that a significant percentage of issues that we're asked to help with turn out to be the result of misconfiguration of a .bashrc and that you can even block your own logins.
In particluar, we recommend that you do not add any of the following to your .bashrc :
- Any commands which load modules
- Any commands which load Python venvs
- Any commands which load Conda evironments
- Any commands which alter your LD_LIBRARY_PATH
If you find yourself in the situation where you're considering doing any of these, please consider contacting us for help before doing so. We may be able to suggest a better alternative and save you hours (or even days) of wasted time trying to figure out why something has broken.
If you need to store large files such as NGS data or to share data with other users on the cluster you can request collaboration projects, which will be set up for you in /project/. Please note that the quota is for all data in all projects and not on a per-project basis. Collaboration projects are a secure way for data to be shared with specific groups of people. You just pick the logical set of data and define the people it needs to be shared with, then we create the project for you and update the list of people as time goes on so that it's always correct. They're a secure, convenient way to share data. For more information, see project(7). To join an exiting project, please ask the PI to contact us via help@imm.ox.ac.uk and ask for your username to be added.
You can additionally share data with other people over the internet using our public datashare service. For further details, see datashare(7).
If you are handling data that needs especially high confidentially (e.g. human patient data) or where there are specific security requirements imposed by the data source or funder (e.g. UK Biobank data), please get in touch with us before uploading it.
Host: cbrglogin1.molbiol.ox.ac.uk
Username: [your CCB username]
Password: [your CCB password]
Port: 22
Then click the Quickconnect button to establish the connection. The files in your home directory on cbrglogin1 will be displayed in the lower right panel of FileZilla. These can be dragged to the left panel in order to copy files from the cluster to your local machine. Similarly, dragging files from the left panel to the right panel will copy them from your local machine to a directory on the cluster.
FileZilla is also installed on the login nodes, and can be used from within an X2Go session. This can be handy for transfering files between the CCB server and any other remote file server (for example, to transfer fastq files from a sequencing facility).
On the CCB servers these files can be found at /databank/igenomes/. More information can be found in igenomes(7)
We recommend taking the time to read modules(7) , python-cbrg(7) and R-cbrg(7) before attempting to run any programs or install software which appears to be "missing".
We also recommend that you send a single question or request per email, and that you always send new requests as new emails and not as replies to old ones. Doing this makes it both more likely that your quick questions are answered quickly, and less likely that your requests are overlooked because we think that we've already done them.