Reference data is imported into a CLC Server using client software, either a CLC Workbench or the CLC Server Command Line Tools. Data to be imported should be copied into an Import/export directory first, from where it can be imported.
If you do not already have the reference data you need, the Reference Data Manager of the CLC Genomics Workbench can be used to download data from QIAGEN servers and some public repositories such as Ensembl to the CLC Server. Further details about this can be found in the section on Reference data management.
Reference data is exported from a CLC Server using standard export functionality of the client software, where the relevant data elements are selected in the Navigation Area of CLC Workbenches, or specified using CLC URLs when using the CLC Server Command Line Tools. Exported data is put into an Import/export directory, from where it should be be moved to a location that can be accessed by the third party tool when it is run.
Import/export directories are configured under the Main tab of the server web administrative interface, as described in Accessing files on, and writing to, areas of the server filesystem.
Data import and export are described in the client software manuals: https://www.qiagenbioinformatics.com/support/manuals/.