Using CLC Genomics Workbench on Turing

Transcription

1 Using CLC Genomics Workbench on Turing Table of Contents Introduction...2 Accessing CLC Genomics Workbench...2 Launching CLC Genomics Workbench from your workstation...2 Launching CLC Genomics Workbench from Turing...3 CLC Genomics Server...6 Server account...6 Connecting to CLC Genomics Server...7 Running jobs...9 Updates...11 Links...11 Information Technology Services High Performance Computing Group 1

2 Introduction CLC Genomics Workbench is a software package supporting bioinformatics work. There are a number of utilities included for analyzing, comparing, and visualizng next generation sequencing data. Accessing CLC Genomics Workbench By default, CLC Genomics Workbench is not installed on ODU workstations. If you would like to install the software on your machine, please send an request to hpc@odu.edu. It is available for Windows, Mac, and Red Hat. This installation utilizes your machine's resources. CLC Genomics Workbench can also be accessed on the cluster. First, you will need a HPC account. This can be requested here under New to High Performance Computing -> Getting an Account. After the account is created, you can login and launch the software. Make sure to have X11 forwarding setup or use a remote desktop (RDP) application. Launching CLC Genomics Workbench from your workstation This depends on your operating system but we usually create a shortcut on the desktop. Double-click the CLC Genomics Workbench icon to launch it. Please note that the CLC_Data directory that shows up in the Navigation Area is stored on your workstation. Also, if this is the first time it launches, you will be prompted to import an example data set. If you click yes, a folder will appear under CLC_Data called Example Data. Information Technology Services High Performance Computing Group 2

3 Launching CLC Genomics Workbench from Turing If you're using a RDP application, we will create a shortcut on your desktop. As soon as you're connected, double-click on the CLC icon. The example below uses SSH with X11 forwarding. 1. Login using your MIDAS credentials. Information Technology Services High Performance Computing Group 3

4 2. From the terminal, type clcgenomicswb7 and press enter. Information Technology Services High Performance Computing Group 4

5 A job will be submitted to the queue and the program will launch from one of the compute nodes inside of the cluster. By typing qstat in the terminal, you can see if the job is in the waiting or running state. Once resources are available, you should see a window like the one below that loads the program and your settings. Information Technology Services High Performance Computing Group 5

6 After it finishes, CLC Genomics Workbench will open. A directory called CLC_Data will be created in your home directory and you should see it in the Navigation Area. If it is the first time you are using it, you will be prompted to import an example data set. If you click yes, a folder will appear under CLC_Data called Example Data. You can download the sample data at any time by going to Help -> Import Example Data. CLC Genomics Server CLC Genomics Server is another piece of software installed on Turing. Some of the key features include centralized data management and scalability. This allows you work in a shared directory and submit jobs to the cluster for additional resources. Server account CLC Genomics Server accounts are separate from MIDAS accounts. The usernames are the same but Information Technology Services High Performance Computing Group 6

7 the passwords are different. If you forget your password, send an to requesting a new one. Connecting to CLC Genomics Server 1. Verify that the client plugin for connecting to the server is installed by going to Help -> Plugins and Resources. 2. Go to File -> CLC Server Login. 3. Fill in the appropriate information and click Login. You will use your CLC credentials. Server host: turing.hpc.odu.edu Server port: 7777 Information Technology Services High Performance Computing Group 7

8 Several group folders will appear in the Navigation Area. You must be a member of the respective group in order to access the folder. Information Technology Services High Performance Computing Group 8

9 Running jobs In order to take advantage of cluster resources, you must move your data into your group directory. Otherwise, your work will be run using local resources. You can click and drag your files from the CLC_Data directory into the group folder in the Navigation Area. Then, you can run your job. Depending on your data and toolbox, you should see a window appear like the one below. From this window, you can choose where you want to run your job. Choosing Workbench is going to run the job from the machine where CLC Genomics Workbench is installed. This might be your workstation or one of the cluster nodes. The CLC Server option is disabled. Information Technology Services High Performance Computing Group 9

10 When submitting jobs to the cluster, you should pick Grid. There will be three choices available in the drop down menu; High, Medium, and Low. The maximum number of slots available for each option is shown below. Maximum Number of Slots High 15 Medium 10 Low 5 Choose whichever option you think is appropriate. If it is computationally intensive, choose Medium or High. For quick, short jobs, choose Low. Continue clicking Next while specifying your options until you click Finish. You should see the status bar at the bottom of your screen. Information Technology Services High Performance Computing Group 10

11 After it initializes and resources are available, your job will run and the progress bar will fill up until it finishes. Updates When an update is available, a window will appear after you launch the application. If you are running CLC Genomics Workbench from your own machine and plan on connecting to the CLC Genomics Server, please be careful. The versions have to be compatible in order to connect. Before the HPC staff pushes an update, an will be sent out to the CLC bio users for notification. Until the update finishes, connections to the CLC Genomics Server will fail. Afterward, the HPC staff will update CLC Genomics Workbench on the cluster and on any workstations. Links 1. CLC bio Website 2. CLC Genomics Workbench Website 3. CLC Genomics Workbench User Manual 4. CLC Genomics Server Information Technology Services High Performance Computing Group 11