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 isclcmainwb.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.