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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
  • Storing data
    • Data structure
  • Special configurations for large amounts of data
    • Temporary data
    • Default Workbench data storage
  • 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

Default Workbench data storage

On all CLC Workbenches, the default folder for storing Workbench data is called CLC_Data, placed under the user's home area.

On CLC Genomics Workbench, there is additionally a default folder for storing reference data^8.1 called CLC_References, placed under the user's home area.

If a default folder is not already present under the user's home area, it will be created on the file system when the Workbench starts up, and the corresponding Workebench file locations will be visible in the Workbench Navigation Area.

The location of default data areas can be changed, which can be useful in a number of circumstances, for example when quotas are applied to user home areas or where roaming user profiles are used. This is done by specifying the folders to use in a file called path.properties and placing this file in the settings folder of the Workbench installation. If this file is in place before the Workbench is started up, folders are not created in the original default locations, but are only created, if not already present, according to the information specified in this file.

Changing the default data locations

The settings for configuring default locations in a path.properties file are:

• datadir For all CLC Workbenches: the full path to the default data location. The folder specified is created if it does not already exist.
• refdir For CLC Genomics Workbench: Either the full path to a folder called CLC_References, or the path under which a folder called CLC_References is present or should be created.

Important: The default data folder (datadir) is fully specified by the path given in the path.properties file, whereas if the reference data area (refdir) does not end with CLC_References, a folder of that name will be created under the path specified.

The following variables can be used when specifying the desired path:

$user

the user name of the current user

$home

the home directory of the current user

$product

the short name of the workbench (clcgenomicswb or clcmainwb)

You can use either forward slashes (normally used on Mac and Linux) or backslashes (normally used on Windows) in the configuration file. The Workbench will use the appropriate type of slash character depending on the platform.

Some examples:

datadir = $home/CLC_Data			(the default)
datadir = X:\clcstorage\$user			
refdir = X:\clcstorage\$user\CLC_References	
refdir = /scratch/$user				(equivalent to /scratch/$user/CLC_References)

You can download a sample path.properties file from
http://resources.qiagenbioinformatics.com/deployment/current/path.properties.

Where Workbench location information is stored

When the Workbench is shut down for the first time, a file called model_settings_300.xml is created in user level settings folder. Data location information is read from this file when starting up the Workbench again.

If the model_settings_300.xml file is deleted, then the next time the Workbench starts up it will again look for the datadir property in the path.properties file.

The location of the model_settings_300.xml file depends on the operating system being used. See User-level information for details.

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Footnotes

... data^8.1

This feature was added in CLC Genomics Workbench 11.0.

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