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• Introduction
  • Deployment strategies
  • Java
  • System requirements
• Installation of Workbenches
  • Getting Workbench installers
  • What a Workbench installer does when launched
  • Installation modes - console and silent
  • Uninstalling a Workbench
• Licenses
  • Connecting to a CLC Network License Manager from Workbenches
• Workbench plugins
• Workflows
• Connecting to a CLC Server
• Security policies
• Storing and backing up data
  • Default Workbench data storage
  • Temporary data
  • Backup of Workbench information
  • Disk space requirements
• System resources
  • Setting the amount of memory available for the JVM
  • Setting the number of cores to use
• Overview - where do we put things?
  • Per-computer Workbench information
  • Per-user Workbench information
  • Per CLC Data Location information

Per-user Workbench information

Workbench user settings

Workbench settings that apply to each user, as well as log files, are found under the user's application data folder. Particularly useful files and areas are described below.

User settings
The usersettings.xml file stores information such as view settings, parameters, workspaces, username and password for CLC Server connections and other settings customized by the user. When an upgraded version of the Workbench is launched for the first time, the user settings file for the most recent older version on the system is copied and used for the new Workbench installation.

The usersettings.xml file is found under:

macOS
/Users/<username>/Library/Application Support/CLC bio/Workbench/ \
settings/<wbname>/<version>/
Linux
<userhome>/.clcbio/workbench/settings/<wbname>/<version>/
Windows 10
C:\Users\username\AppData\Roaming\CLC bio\Workbench\ \
Settings\wbname\version\

Data Locations
Information about data locations a user has added via the Workbench Navigation Area is stored in the model_settings_300.xml file, found under:

macOS
/Users/<username>/Library/Application Support/CLC bio/Workbench/settings/
Linux
<userhome>/.clcbio/workbench/settings/
Windows 10
C:\Users\username\AppData\Roaming\CLC bio\Workbench\Settings\

Workbench log files

Log Files
If problems arise, log file are useful to our Support team for troubleshooting the issue. How to contact the QIAGEN Bioinformatics Support team with the relevant log information is covered in our FAQ area at https://qiagen.my.salesforce-sites.com/KnowledgeBase/KnowledgeNavigatorPage?id=kA41i000000L5r9CAC.

If you wish to investigate the logs yourself, the key log files are called clc-workbench.log, output.log and error.log. These files can be found under:

macOS
/Users/<username>/Library/Application Support/CLC bio/Workbench/log/
Linux
<userhome>/.clcbio/workbench/log/
Windows 10
C:\Users\username\AppData\Roaming\CLC bio\Workbench\log\

Installed workflows

Installed workflows are saved under:

macOS
/Users/<username>/Library/Application Support/CLC bio/Workbench/ \
workflows/<wbname>/<version>/
Linux
<userhome>/.clcbio/workbench/workflows/<wbname>/<version>/
Windows 10
C:\Users\username\AppData\Roaming\CLC bio\Workbench\ \
workflows\wbname\version\

Proxy settings for downloading SRA reads

Proxy settings for downloading reads from SRA via the Search for Reads at SRA tool in the CLC Genomics Workbench must be configured per-user. This is in addition to the proxy settings defined in the Workbench Preferences that are described in Per-computer Workbench information.

Configuring the proxy settings for downloading reads from SRA interactively is described in the CLC Genomics Workbench manual. To configure these settings in a hands-off manner:

• Run the vdb-config command located in the Workbench installation area as the user who will be downloading reads from SRA, using the --proxy option:

  <$WBINSTALLATION>/exec/vdb-config --proxy <http://your.proxy.server:port>

  OR

• Create a file with the proxy settings that can be placed in each user's home area:
  1. Configure the proxy settings for a single user as described in the point above, or interactively as described in the CLC Genomics Workbench manual.

     This edits (or creates, if not already present) a file in that user's home area, $USERHOME\.ncbi\CLC\user-settings.mkfg, that contains the proxy settings.

  2. Remove any user-specific lines in that file.

     The values for the user-specific entries in that file are default locations. I.e. the same locations used as when this file is not present. Thus removing these lines should have no impact.

  3. Place a copy of this edited file in the relevant user area(s) on the systems the CLC Workbench is installed on.

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