CLC Genomics Workbench

MSI will no longer support CLC software staring 09/18/2016

 

CLC Genomics Workbench (CLCGWB) is a cross-platform desktop application and graphical user interface for visualizing and analyzing next-generation sequencing data. When CLCGWB is combined with the CLC Genomics Server (CLCGS), as it is at MSI, analyzes that would take too much memory or too long to run interactively or on your own computer can be submitted to the lab queue.  More information about CLCGWB can be found at http://www.clcbio.com/products/clc-genomics-workbench/

Tips for using CLCGWB at MSI can be found here:
https://www.msi.umn.edu/content/using-clc-genomics-workbench

This software is limited to 10 concurrent users and 9 concurrent jobs running on the lab system.

Accessing CLC Genomics Workbench (CLCGWB) and CLC Genomics Server (CLCGS) with NICE

  1. Get a MSI Account (https://www.msi.umn.edu/getting-started)
  2. Link your MSI account to CLCGS by linking your group to CLCGS. Email help@msi.umn.edu with Connect my MSI account to CLC Bio in the subject line. Include your username, your group name or if you don't know your group name the name of your PI. Important: your group only needs to be linked to CLCGS once. If someone in your lab/group already has access to CLCGWB and CLCGS then you will also have access with your MSI account.
  3. Navigate your web browser to https://nice.msi.umn.edu/ and login using your MSI username and password. 
  4. If this is your first time using NICE download and install the DCV client from the top left corner of the screen. 
  5. If you have the DCV client installed already select one of the non-GPU options from the bar on the left of the screen. 
  6. Once your NICE session has stared a file will be downloaded. Open the file, should have a .vnc ending.
  7. Once your NICE session has started open the terminal application. 
  8. Type "module load clcgwb" then hit return.
  9. Type "clcgenomicswb8" then hit return to lauch the application.

Accessing CLC Genomics Workbench (CLCGWB) and CLC Genomcis Server (CLCGS) with NX

  1. Get a MSI account (https://www.msi.umn.edu/access/signup)
  2. Link your MSI account to CLCGS by linking your group to CLCGS. Email help@msi.umn.edu with Connect my MSI account to CLC Bio in the subject line. Include your username, your group name or if you don't know your group name the name of your PI. Important: your group only needs to be linked to CLCGS once. If someone in your lab/group already has access to CLCGWB and CLCGS then you will also have access with your MSI account.  
  3. Download, install and configure NX client. (https://www.msi.umn.edu/content/nx-client-configuration) You must use NX client to access CLCGWB at MSI remotely or you can come use the computer lab in Walter 575. 
  4. NB: Do not access a GPU node to start a workbench session. The workbench can only access the CLC server if the workbench application is started on a non-GPU node. 
  5. Open an NX client session using a GNOME virtual desktop and your MSI account. 
  6. Within the NX session open a terminal
  7. In the Terminal:
    Type: "isub -m 15gb -w 2:00:00" then hit return
    When prompted enter your MSI account password then hit return
    Wait for job to start
    Optional alternative: Use NICE to obtain an interactive session once you lauch the session open a terminal and start at step 7. 
  8. Type: "module load clcgwb" then hit return
    Type: "clcgenomicswb8" then hit return
  9. CLCGWB will start up 
  10. Once CLCGWB is open configure the server connection:
    In the top left corner under "File" select "Server Login"
    Enter your MSI user name and password
    Open the advanced options by clicking the triangle
    In the "Server host" section type "localhost"
    In the "Server port" section type "7777"
    Check the boxes for save username and automatic login
  11. Once connected to the server you will see your group's folder in the navigator on the left side of the CLCGWB. You will have access to anything in your group's folders and to the files within the data folder. 

 

NX Client Tips:

If you are having issues with the display in your NX client change the display options by mousing over to the top right corner of your NX client window (close to the green man). Click on the folded over corner that appears. Select "Display",  then turn off "Keep Original Aspect" and turn on "Resize Remote Screen". Next, select "Change Settings" and set the "Quality" slider to the maximum (+). 

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