Using your CBRG bioinformatics account

The following information should allow you to log in to our server, "deva", using your CBRG account.
We recommend using the NX remote desktop to access deva, particularly if you are new to using the command line interface. A connection via NX to the CBRG server will create a virtual desktop - allowing you to run x-windows-based graphical tools as well as command-line tools. Instructions on how to set this up are below. If you have any problems making a connection please contact CBRG.
If you are already familar with using a CLI you can access the servers via SSH.

These guidelines are for Full CBRG accounts only. Users with a CBRG-Proteomics account may use their username / password to access mascot.

NX remote desktop
NX is a remote desktop program which lets you to connect to a remote server and run graphical applications remotely on that server. Your local machine acts like a terminal on the remote server. For some large graphical applications such as seqmonk, the performance can be greately improved because everything runs on the server. This is more noticable if you are connecting to the server over a slow network link. NX connections are secure as they use SSH encryption and authentication.
Using NX on a PC

To install NX Client on your Windows machine download and install the nxclient package

Once the package has installed, open NX Client:

This should open the NX Connection Wizard:

Enter a Session name and Host Address:


Choose 'GNOME' from the drop down menu:

Click the 'Show the Advanced Configuration dialog' box:

Click the 'Key...' button:

A new window will open:

You will need one of the CBRG SSH server keys.
Click this button and copy the appropriate key:

Get CBRG server keys

Replace the existing key with the copied server key.
Then click 'Save'

Login with your CBRG username and password:

A new window displaying the Deva remote desktop will appear:

To add Open Terminal shortcut to the menu bar, first click 'Applications' then 'System Tools' then right click on 'Terminal'

This will open a sub menu - choose 'Add this launcher to panel'

This will put an icon on the top menu bar - click this to open a 'Terminal' window:

NX remote desktop
NX is a remote desktop program which lets you to connect to a remote server and run graphical applications remotely on that server. Your local machine acts like a terminal on the remote server. For some large graphical applications such as seqmonk, the performance can be greately improved because everything runs on the server. This is more noticable if you are connecting to the server over a slow network link. NX connections are secure as they use SSH encryption and authentication.
  • NoMachine, NX client (recommended) Please use this link to download the package v5.3.12. Note that the latest version 6.0.66 will NOT work with the CBRG servers.
  • OpenNX, NX client (alternative)
NX for Mac OS X 10.7 or later

To install NX Client on your Apple Mac OS X machine use this link to download the package:

Once the package has downloaded, install the application by double clicking on the .dmg file:

Double click on the .pkg file:

Click Continue:

Click Continue:

Click Install:

Click Close:

Download a server key file - you will need this during the next configuration steps:
Get CBRG server keys


Next, open the Application and you should see a screen like the one below - Click "New" to establish a new connection:

Select SSH as the protocol and click continue:

Type in the host name and click continue:

Select "Use the NoMachine Login" and click continue:

Tick the "Use an alternate Server Key" and browse for the deva_key file you downloaded earlier. Click continue:

Choose "Don't use a proxy"

Choose a name for the connection e.g. 'deva' and click "Done"

Now double click on the "deva" icon

Log in with your CBRG username and password:

The following steps need only be set once if you choose the tick boxes to "Save this Setting in the connection file". Choose "Create a GNOME virtual desktop":

You should see the virtual desktop appear. To create a shortcut to terminal, from Applications menu, choose "System Tool - Terminal", then right click and choose "Add this launcher to panel".

Click on this "Terminal" icon to open a terminal window

Install Open NX on a Mac machine

Open NX Client for Mac

To install Open NX on your machine follow the link here , and download the package using the 'Download' link on the left:


Click on the link to download the version for MacOSX:


Now double click the dmg file you have just downloaded (probably in your 'Downloads' folder):

Double click on 'OpenNX' icon:


Follow the instructions in the installer:

Enter your local machine password to allow installation:


Download a server key file - you will need this during the next configuration steps:
Get CBRG server keys


Now go to the 'Applications' folder and open 'OpenNX' folder then double click on Connection Wizard:


You will see a warning window - just click OK whenever you see this:

Click 'Next':


Enter the session name and host address:

Choose GNOME from the drop-down menu:


Click Next:

Tick the Show Advanced Configuration dialog button:

Click the Key button and enter the 'key' that you downloaded earlier - make sure there is no extra spaces or returns at the end


Open the OpenNX application from the Appliactions-OpenNX folder

Enter your CBRG username and password:

A new window displaying the Deva remote desktop will appear:


To add Open Terminal shortcut to the menu bar, first click 'Applications' then 'System Tools' then right click on 'Terminal'


This will open a sub menu - choose 'Add this launcher to panel'


This will put an icon on the top menu bar - click this to open a 'Terminal' window:

Step 1. Install SSH

The SSH client for PC's (SSHSecureShellClient-3.2.9.exe) is available for download. Once downloaded, this application will install the SSH client on your PC. Note: you need to have administrator rights on the machine to be able to do this (or contact your local IT support to do it for you). After installation, the following guides should help you set up SSH to connect to your CBRG account.

Step 2. Configuring SSH on a PC

Once you have installed the SSH client, you will be able to start SSH (via "SSH Secure Shell" in start > all programs) before setting it up to connect to the server.

  • click "Profiles" (see Fig 1)
  • click "Add Profile..."

SSH click on "Profiles" Fig 1. Configuring SSH client


  • type a name for the new profile (e.g. deva) (see Fig 2)
  • click "Add to Profiles"

Adding a new SSH profile Fig 2. Adding a new SSH profile


  • again, click "Profiles"
  • click "Edit Profiles..."
  • next to "Host name", type: deva.molbiol.ox.ac.uk (see Fig 3)
  • next to "User name", type your CBRG username

Add CBRG address and username Fig 3. Add server address and username


  • Click "OK" to close the "Profiles" window
  • finally, click on "File" and then "Save Settings"

The SSH client is now configured to allow a secure connection to the server, deva.

Step 3. Guide to using SSH and SFTP

Connecting - A connection to CBRG can be made by clicking on Profiles and selecting "deva". You will be prompted for your CBRG account password.

Terminal Window - When a successful connection has been made, the terminal window will display a welcome message (see below) to let you know. If required, further terminal windows can be brought up by clicking the SSH term icon icon.

  
                       *** Welcome to the Computational Biology Research Group *** 
                
                     -------------------------------------------------------------------
                     *  If you find ANY problems with the service please E-mail genmail * 
                     -------------------------------------------------------------------
                

Secure File Transfer - You can use the SSH client to securely transfer files between your PC and your home directory on the server. Clicking on the secure file transfer icon icon will bring up the secure file transfer window (see Fig 4). This window will display the directory structure of your PC in the left pane and the directory structure of your home directory on deva in the right pane. Files can be dragged and dropped between the two systems. You can alter the read-write-execute permissions of any files on deva by right-clicking the file in the right pane and selecting "Properties".

SSH Secure File Transfer Window Fig 4. SSH Secure File Transfer Window


Disconnect - The disconnect icon disconnect icon should be used to break the connection with the server prior to closing the SSH client (or if you leave your PC unattended).

Connect via X11

Using X11 to log into CBRG servers from Mac OS X - although it is possible to connect to CBRG servers using the simple terminal application (Applications/Utilities/Terminal) we recommend using the x-term for all connections. This will allow you to gain maximum use of the software available via your CBRG account.

  • Start X11 (from "Applications" and then "Utilities")
  • Within X11, open a new xterm window by choosing "Applications" and then "Terminal".
  • To connect to CBRG type the following and press the return key:
    (Note: in the example below, the -Y is upper-case, and the -l is a lower-case 'L' )
    ssh -Y -l username deva.molbiol.ox.ac.uk
Setting up X11 for 10.6, 10.7 and 10.8

Click here to download X11 2.7.4 for OS X 10.6.3 or later

Further details regarding X11 for Mac OS X can be found at the Apple website.



Use the following set of instructions to install X11.


Double click on the XQuartz.pkg icon to open the installer:

X11 1

X11 2

When prompted click "Continue"

X11 3

X11 4

X11 5

X11 6

X11 7

The X11 application will be installed in "Applications - Utilites"

X11 8


Fugu (SFTP and SCP)

Fugu (SFTP and SCP) on OS X

Fugu is a graphical frontend to the commandline Secure File Transfer application (SFTP).

Please note that the current release of FUGU is not compatible with Lion (Mac OSX 10.8). Please install the Universal Binary if you are using Lion (10.8) or Mountain Lion (10.7) - click here to download the Universal Binary

Drag the Fugu icon to your Applications folder, then double click to run the program. This will display a window listing the files in your current working directory (/login/your_account):

Fugu connections screen


Enter the connection details as shown below (giving your CBRG account name), click the Add to favourites button to add these settings to your Favourites list, then click Connect:

Fugu connections screen - add CBRG account name


If logging on for the first time a similar message to the following will then be displayed:

The authenticity of host 'deva.molbiol.ox.ac.uk' can't be established.

Unable to get host key. Something to odd.

Are you sure you want to continue connecting?

When you see this you should click on continue


This message is only displayed the first time you connect to a site. Click Continue. You will then be prompted for your CBRG password:

Fugu password prompt


Enter your password and click Authenticate. The connection to CBRG will then be established and a window will open displaying your files on the server:

Fugu file list


To transfer files simply drag-and-drop between windows.

Use Fugu/Quit Fugu on the menu bar to exit the software.

Fugu (SFTP and SCP)

Command Line SFTP on Mac OS X

SFTP comes as standard on Mac OS X systems and can be accessed via the command line from the x-term (see above). Access to CBRG can be achieved via the command line command (It is necessary to press the Return key after entering each command.):
sftp login_name@deva.molbiol.ox.ac.uk

SFTP commands:

  • help to display a list of available commands. The default directory on the Macintosh will be the top level of your user account /home/your_group/your_account.
  • lls can be used to list the contents of the local (Macintosh directory).
  • lpwd will print the local directory.
  • pwd prints the remote (CBRG) directory.
  • put is used to upload a file from the Macintosh to the server, for example:
    put local_filename server_filename
  • get is used to transfer files from the server to the Macintosh, for example:
    get server_filename local_filename
  • bye to exit.