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2.12. How can I delete a whole data location and all its contents?
For CLC Genomics / Main Workbenches and Biomedical Genomics Workbenches:
Before removing the data files and the data location(s) hosted by the CLC Workbench software, please make sure that the data have been properly backed up and stored to avoid data loss due to accidents.
While the CLC Workbench software is closed, copy the data folder over to the new storage area to be used with filesystem tools such as copy and paste. Once the data files are in place, please start the CLC Workbench, then add the new CLC data location based on the instructions at
and then point this data location path to the data folder that was just copied over.
You can then set the default CLC Data location to the new location within the Workbench. More information about setting the default data location is available at
Once the default data location has been assigned to the new partition, you can simply remove the old data location by right clicking on the location folder in the navigation area and choose Location | Remove Location.
Before you delete the original CLC Data folder from the filesystem, please do the following to verify that the data in the new location are working as expected:
a. rebuild the data index
- Go to the topmost folder in the location tree on the left hand side of the Workbench, under which the object in the error report is stored.
- Right-click on this folder.
- In the menu that appears, choose Location.
- Choose to Rebuild index.
- Once the process is completed, restart the Workbench software.
b. run a couple of analysis with the data from the new location as input, and then save the data into the new data location to verify that the software have both read and write access to the data folders on the new partition. For example, run the Create Sequencing QC Report tool on the imported read data and save the report into the new location
2. Remove the temporary folder to the new partition
You can find out which location your Workbench is writing temporary files to by going to
Help | About CLC Genomics Workbench
and then clicking on the "File locations" tab.The default temporary data location may contain data required from other non-CLC applications. You can remove the CLC temporary data by deleting the sub-folders with names starting with "CLC-" while the Workbench is closed.
For CLC Genomics Servers:
Before removing the data files and the data location(s) hosted by the CLC Server software, please make sure the data have been properly backed up and stored if they are needed in the future.
You will need to be able to log into the Genomics Server web-based thinclient with privileged account (e.g. root) on the CLC Server to do this.
After logging in as root, the data folder or directory path(s) can be found under Admin | Main configuration | File system locations
Please record the paths and then remove the locations by using the "Remove Location" button next to each data location path.
After the changes to the data locations have been saved, and that the CLC Server service is restarted, you can then proceed to remove the data folder or directory on the filesystem of the same paths previously configured on the Genomics Server.
More information on the data location of the CLC Server is available in the following manual link:
The temporary data location is either located on the system default (e.g. /tmp on linux) or in a customized path specified in the CLCGenomicServer.vmoptions file found under the software installation location. While the server service is closed, you can then remove the sub-folder within the temporary location with the name starting "CLC-".
If you wish to redirect the temporary folder for the single server or the job node setup, follow the instructions described in
For the Genomics Server running grid integration as the backend, please locate the grid worker temporary location by referring to the instructions in