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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

Default Workbench data storage

The default CLC location for storing data in Workbenches is called CLC_Data. An additional default location, CLC_References, is primarily intended to store reference data downloaded or imported using the CLC Genomics Workbench's Reference Data Manager. Folders of these names are created in the user's home area when the Workbench is started up if they do not already exist.

Changing the default data location for a single user from within a running Workbench is described at http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Data_structure.html. Changing the location of the CLC_References folder for a single user from within a running CLC Genomics Workbench is described at http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=References_management.html.

The remainder of this section describes making changes that apply to all users of a given Workbench installation.

Changing default data locations for a Workbench installation

The location of default Workbench CLC locations can be specified in a file called path.properties placed in the settings folder in the Workbench installation area. If this file present before the Workbench is started up, the folder(s) to use as default locations are created in the locations specified in that file.

The relevant settings in the path.properties file are:

• datadir Used to specify the full path to the default data location to use (instead of CLC_Data).
• refdir Used to specify the full path to a folder called CLC_References. Any path provided that does not end in CLC_References will have a folder called CLC_References created under the folder specified. Relevant only for CLC Genomics Workbenches.

To completely avoid the creation of the original default locations CLC_Data and CLC_References on a system where CLC Workbenches have not previously been run:

• Install the Workbench but do not start it up.
• Place the path.properties file with the data location information in the settings folder in the Workbench installation area.
• Start the Workbench.

On start up, the Workbench will look for the data location settings in the path.properties file. If the default folder(s) specified in that file do not already exist, they will be created.

To update default data locations on systems where CLC Workbenches have been run previously:

• Ensure CLC Workbenches are not running on the system.
• Delete the model_settings_300.xml located in the user level settings folder for each Workbench user on the system.
• Place the path.properties file with the data location information in the settings folder in the Workbench installation area.

On start up, the Workbench will look for the data location settings in the path.properties file. If the default folder(s) specified in that file do not already exist, they will be created. Folders on the file system created by the Workbench earlier, e.g. CLC_Data and CLC_References folders in user home areas, will need to be manually deleted if they are no longer needed.

Note: The model_settings_300.xml file contains the locations of all CLC Workbench data locations. If you delete this file, then any non-default locations will need to be manually added to the Workbench again.

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.

Examples:

datadir = $home/CLC_Data
datadir = X:\clcstorage\$user			
refdir = X:\clcstorage\$user\CLC_References	
refdir = /scratch/$user

In the above examples, the first is the standard default for a CLC Workbench. The last is equivalent to specifying /scratch/$user/CLC_References.

A sample path.properties file is available from
https://resources.qiagenbioinformatics.com/deployment/path.properties.

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