Using CLC Genomics Workbench

Why Use CLC Genomics Workbench at MSI?

   By using CLC Genomics Workbench (CLCGWB) at MSI you gain access to the licenses purchased by MSI and MSI computational resources. If you were to run CLCGWB from your personal or lab computer you would need to purchase your own license from CLC Bio and you could only use the computational resources built into that specific computer. 

What do you need to do to use CLCGWB at MSI?

    You need an MSI account with a large enough memory quota to allow for the type of data you will be using to analyze in CLCGWB. Information about how to get an MSI account can be found here (https://www.msi.umn.edu/access/signup). You need a basic account to use CLCGWB.   
    
If you have data on a personal or lab computer that you would like to use within CLCGWB you can copy it into your MSI directory using WinSCP (Windows) or Cyberduck (Mac OSX). 

Download and install either WinSCP (http://winscp.net/eng/download.php) or Cyberduck (http://cyberduck.en.softonic.com/mac). Once installed you can connect to your MSI directories using SFTP.
Server: login.msi.umn.edu
Username: your MSI account username
Password: your MSI account password

Where Can I Get Help?

    You can access tutorials and the CLCGWB manual from within CLCGWB from the Help menu. Or you can access the manual and tutorials online at the CLC Bio support website (www.clcsupport.com). If you have questions regarding use of CLCGWB or you receive error messages you should first contact CLC Bio support, which can be done though the Help menu. If you are having trouble connecting to CLCGWB or CLCGWB crashes then email MSI at help@msi.umn.edu.

How Do I Get My Data Into CLCGWB?

  Using the import function built into CLCGWB will give you access to your data stored in your MSI account directory. If you are importing sequencing data use the import tool that corresponds to that type of data i.e., Illumina. Annotation data such as BED, GTF/GFF, WIG or VCF files should be imported using the Track import tool. You will need to have the reference genome downloaded to CLCGWB already.
More information:
http://www.clcsupport.com/clcgenomicsworkbench/current/index.php?manual=...

Where Is My Data When I Export It?

  Each group has a space that exported data is automatically saved to. The group name will be your PIs MSI account name and the same name as the folder in CLCGWB where you can save you data. You can use Cyberduck or WinSCP to download this data to a personal or lab computer the same way you access anything else saved in you MSI account. If exporting data from a folder with a blue dot you will need to use the Grid. The 15GB, 2 core setting should work for most export jobs. 
Path to exported data:
/home/groupname/clcbio/importexport/groupname

More information:
http://www.clcsupport.com/clcgenomicsworkbench/current/index.php?manual=Import_export_data_graphics.html

Where To Run?

  For some of the tools in CLCGWB you will be asked to specify where to run your analysis. You will be able to select from three options: Workbench, CLC Server or Grid. Never use the CLC Server, if you try to analyze data on the server you will get an error. In general use the Workbench for quick tasks that don't have large memory requirements. Use the Grid for any job that may take more than a few minutes or need more than 15 GB of memory.  When you run analysis on the Grid they will continue to run even if you close CLCGWB. You can monitor the progress of the analysis in the processes tab at the bottom of the navigation area. 

Use the Grid if:
Exporting data from a folder with a blue dot
Mapping NGS data - 30GB, 4 cores
RNA-Seq Analysis - 60GB, 8 cores
Blast - 30GB, 4 cores
ChIP-seq - 30GB, 4cores
​Variant Detection - 60GB, 8 cores
Importing NGS data- 15GB, 2 cores

Use the Workbench if:
Using Track Tools
Filtering Data
Annotating Data

Grid Job Did Not Run Successfully

If you run a job on the Grid and you get an error stating that your job did not run successfully try running the same analysis again with more memory. If you used 30GB the first time and got this error try again with 60GB. If you run the job with 120GB and still get this error please send a message to help@msi.umn.edu

What Did I Do When I Typed isub?

  You started a computer that will have 15GB of memory (-m 15gb) and will run for 2 hours (-w 2:00:00). After 2 hours your CLCGWB session will end so if you need more time change the –w option to reflect what you need (ex: 3 hours would be –w 3:00:00). In general, you shouldn’t start CLCGWB with more than 15GB of memory. If you are going to run an analysis that needs more memory you can submit that job to the Grid.