Temporary data

General information about temporary files

CLC Workbenches write temporary files to disk during many analyses. Depending on the data set, these files can take up a lot of disk space. By default, these files are written to the standard location for temporary files on the system. If space there is limited, a different location can be specified.

Important: Performance is heavily dependent on constant, fast access to temporary files. Thus, the location designated for temporary files should be on an internal drive on the system the Workbench is installed on. Locations accessed over a network connection or locations on an external drive are not appropriate for this purpose.

Configuring a non-default location for temporary files

For changes to settings to take effect, the Workbench must be restarted after the changes are made.

Recommended method

To configure a non-default location for temporary files, add the following setting to the vmoptions file for the Workbench: 

	-Djava.io.tmpdir=</path-to-temp>

Replace </path-to-temp> with the absolute path to the new location.

The location of the vmoptions file depends on the operating system:

Windows and Linux
The file is located directly under the installation area of the Workbench. For the CLC Genomics Workbench, the filename is clcgenomicswb.vmoptions. For the CLC Main Workbench, it is clcmainwb.vmoptions.

macOS
The file is located in the application bundle and is called vmoptions.txt.

To find this file, navigate to the Workbench application in a Finder window. Right-click on the application, or click on it while holding the Ctrl key down (Ctrl + click), and choose "Show Package Contents" from the menu that appears. The file is within the Contents folder.

A second method

Adding a setting to a properties file can also change the location temporary files are written. Note however that using this method, certain files are still written to the default location when using CLC Genomics Workbench 25. This is unlikely to be problematic unless the default temporary area is very small, but due to this, this method will not be supported from version 26.

Create a text file, or edit an existing file, called path.properties in the settings folder under the Workbench installation directory. Ensure the filename does not have an additional extension, e.g. ".txt".

In the path.properties file, add a line like: 

	tmpdir = </path-to-temp>
replacing </path-to-temp> with the absolute path to the new location.

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