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CLC Genomics Workbench

Before You Begin

Email scinet_vrsc@USDA.GOV so that the admins can setup the import/export directories and permissions for access.

We need the following information:

  1. Path to your project directory.
  2. Any additional users that are part of the said project.

Access CLC Genomics Workbench via Open OnDemand

Step 1: Access Open OnDemand:

  • Open your web browser and navigate to the Open OnDemand login page provided by SCINet
  • Link to Open OnDemand User Guide: https://scinet.usda.gov/guides/access/open-ondemand
  • Log in using your SCINet credentials to access the Open OnDemand dashboard

Step 2: Launch CLC Genomics Workbench via Open OnDemand:

  • Return to the Open OnDemand dashboard and click on the “Interactive Apps” section. OpenOnDemand1

  • Look for the “CLC Genomics Workbench” app and click on it to launch the Workbench.

Step 3: Connecting to CLC Server:

  • After launching CLC Genomics Workbench, you will see the main interface with various tools and functionalities. Connections

  • To connect to CLC Server, go to “Connections” -> “CLC Server Connection.”

    ConnectionsServer

  • A dialog box will appear for server configuration. Depending on your network setup, choose the appropriate server configuration: CLCServerConnection

CLC Server Login

  1. File -> Connections -> CLC Server Connection
  2. Server Name and Port
  • If connecting via Ceres Open On Demand 
    Server name: 10.1.9.210
Server port: 7777
  • If connecting from elsewhere 
    Server host: 199.245.99.12
Server port: 7777
    1. Username and Password(GA code not required)
  1. Log in.

screenshot of CLC Genomics Workbench 22.0.2 software homescreen

After successful login, you should see a directory CLC-<your project> in the top left window.

CLC Grid

screenshot of CLC Genomics Workbench 22.0.2 Server Options

Grid can be used to run tasks on Ceres compute nodes, users also have the option to select the slurm queue.

CLC discussion group on Scinet Forum

Scinet Forum has a discussion group for CLC users at https://forum.scinet.usda.gov/c/special-topic-discussion/clc/14

Current Licenses on Ceres

CLC Workbench - 3 CLC Grid - 4

If the license requests exceed the number of seats - CLC Workbench will open in read-only mode - The CLC Grid waits for existing jobs to complete and then launches your job.