HOWTO - CLCBio Genomics Workbench on the BDUC cluster

In order to run this software on your personal Mac/PC, you will have to download the software directly from CLCBio, install it appropriately for your platform, and then point it at the Biochemistry license server which will allow you to check out a token to run it. The workbench will ask you to identify it when it starts up, but if you miss it on the 1st startup or need to change it, you can edit the License Server configuration by clicking:

Menu item HELP → License Manager → Configure Network License → click Manually specify license server and provide the information shown below:

If the image above is missing, the required info is shown below in text form

Where the CLC package differs from the available Lasergene is in its capacity is that UCI has also licensed the CLC Genomics Server Assembler, which provides an integrated multicore assembler functionality, supporting the Illumina format among others. The machine hosting it on the BDUC cluster has four 64bit Opteron cores and 64GB RAM, so it should have sufficient resources to handle most assemblies.

There are 2 ways to use the CLC software.

The following describes how to run it on the BDUC machine.

If you use Windows, you’ll need to set up both PuTTY (to provide the ssh software) and Xming (to provide the X11 software). Both of them are free and freely distributable - you can legally give them to anyone.

Xming provides the X server that displays the X11 GUI information that comes from the Linux machine. When started, Xming looks like it has done nothing, but it has started a hidden X11 window (note the Xming icon in the toolbar). When you start an X application on the Linux server (after logging in with PuTTY as described below), it will accept a connection from the Linux machine and display the X11 app as a single window that looks very much like a normal MS WinXP window. You’ll be able to move it around, minimize it, maximize it and close it by clicking on the appropriate button in the title bar. There may be a slight lag in response in that window, but over the University network, it should be be acceptable.

PuTTY is an ssh terminal connection that allows you to securely connect to the Linux server and interact with it in a purely text-based basis. For shell/terminal cognoscenti, it’s considerably less capable than any of the terminal apps (konsole, eterm, terminator, etc) that come with Linux, but it’s fine for establishing the 1st connection to the Linux server. Since the CLCBio genomics Workbench requires an X11 GUI, you’ll need to configure PuTTY to do X11 forwarding.

To enable this, double-click the PuTTY icon to bring up the PuTTY configuration window. On the left Pane, follow the clickpath:

Connection → SSH → X11 → check the "Enable X11 Forwarding" box.

After setting this, click on Session at top of the pane, and set a name in Saved Sessions on lower right pane, click the [Save] button to save the connection information so that the next time you need to connect, the correct setting will already be set.

To reiterate, you’ll need to be running both Xming and PuTTY to be able to use the CLCBio GUI. There are videos here and here describing this process for those who would rather not read.

If you use a Mac, you’ll need to install the X11 software that comes with the OS. The MacOSX installation DVDs come with a free, Apple-certified X11 installation. On Leopard, it’s in Optional Installs → Optional Installs.mpkg All you have to do is install it and start it running in the background to accept the X11 windows (Applications → Utilities → X11).

Then start the Terminal app and log in as shown below. Note that you have to use the -Y flag.

For a more in-depth tutorial, Apple has a longer tutorial as well.

If you use Linux, you should be good to go already. These tools and packages are already installed on all popular distributions of Linux.

If you do not want to use the BDUC login node, you can log directly into the claw6 node by entering the following line into your terminal application (Mac & Linux):

If you are using the putty application, you will have to first log into the bduc-login node and from there, log into claw 6.

ssh assumes you want to use the same login ID and claw6 has been aliased to the correct machine.

This free software enabled you to start and maintain a Desktop connection to claw6, even when you disconnect (for example, to close your laptop to go home or even abroad). It’s somewhat complicated to set up but it gives usable performance even across continents (most of the time). Please see the BDUC HOWTO on the NX clients.

When you start this connection, you’ll need a terminal application on the remote desktop and then continue as described below. To open a terminal session from the KDE desktop, right-click → Run Command → then type konsole (without the quotes), and then click on the konsole terminal app that appears below the search bar.

If you want to start the CLCBio app directly, jut type CLC into the Run Command search bar and the 2 CLCBio clients will appear as options. Choose the one you want.

Once you have logged into claw6, the process is identical for all clients.

The system will spew some informational lines and the identify itself as claw6 like this:

If you’ve done everthing right, the CLCBio splash screen will pop up and shortly thereafter you’ll see the whole application window. It has already been directed to the Biochemistry license server.