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CLC Genomics Workbench
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:
This software is limited to 10 concurrent users and 9 concurrent jobs running on the lab system.
Accessing CLC Genomics Workbench (CLCGWB) and CLC Genomcis Server (CLCGS)
- Get a MSI account (https://www.msi.umn.edu/access/signup)
- Link your MSI account to CLCGS by linking your group to CLCGS. Email email@example.com 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.
- 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.
- 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.
- Open an NX client session using a GNOME virtual desktop and your MSI account.
- Within the NX session open a terminal
- 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.
- Type: "module load clcgwb" then hit return
Type: "clcgenomicswb8" then hit return
- CLCGWB will start up
- 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
- 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 (+).