Reference data management
Some functionality requires a Server File System Location called CLC_References. Examples include:
- Submitting workflows for execution via a CLC Server, where those workflows are configured to use QIAGEN reference data.
- Submitting workflows for execution via a CLC Server, where one or more inputs have been defined with workflow roles.
- Downloading or importing data to the server using the CLC Genomics Workbench Reference Data Manager.
General information about the CLC_References server location
- A file system folder named CLC_References must exist, meet the certain requirements, and then be configured as a Server File System Location.
- By default, a CLC_References File System Location has special permissions applied, allowing all CLC Server users to download or import data to this location, with only admins permitted to delete data from it. Further details about the default permissions on this location are provided in the Working with a CLC Server CLC_References location section below.
- The default configuration if group-level permissions are enabled on the CLC_References location is that only members of the admin group can download or import data to this location. Both read and write permissions are required for other groups that should be given permission to download or import data here. The Apply to all subfolders checkbox should be checked when changing permissions for this location.
No matter the permissions set, only admins are able to delete data from this location.
Working with a CLC Server CLC_References location
Using the default configuration of a CLC_References File System Location, where permissions have not been explicitly enabled by a server administrator, the following permissions apply:
- Reading All data stored in this location can be viewed and used by all users logged into the CLC Server.
- Writing
- Data can be added to this location by any user logged into the CLC Server via a CLC Genomics Workbench using the following functionality:
- The launch wizard of a workflow that supports selection of a Reference Data Set.
- The View Reference Data wizard opened from the QIASeq Panel Analysis Assistant.
- Download and import tools provided in the CLC Genomics Workbench Reference Data Manager.
- Data can be added to this location by a member of the admin group logged into the web client by downloading reference data for an installed workflow that requires QIAGEN reference data.
- Data cannot be placed in the CLC_References File System Location using standard mechanisms such as copy/paste, saving analysis results, etc.
- Data can be added to this location by any user logged into the CLC Server via a CLC Genomics Workbench using the following functionality:
- Deletion
- Deletion via a CLC Genomics Workbench
Data can be deleted only by members of the admin group, and only using functionality provided in the Reference Data Manager. Data deleted from the CLC_References location this way is deleted immediately. I.e. deletion does not require a server admin to take a separate action to empty a recycle bin.
Data cannot be deleted from this area using standard mechanisms, such as deleting elements in the Navigation Area.
- Deletion via the web client
Data can be moved to the Recycle Bin by any user using functionality under the Element Info tab. Data in a user's Recycle Bin can be deleted by that user unless recycle bin restrictions have been configured.
- Deletion using CLC Server Command Line Tools
Data can be moved to the Recycle Bin by any user using the
rmcommand. Only members of the admin group can use the empty_recycle_bins command.
- Deletion via a CLC Genomics Workbench
Additional information about the CLC Server CLC_References location
- When installing workflows requiring QIAGEN reference data on the CLC Server, an administrator can download that data via the web client. If this is done when no CLC_References File System Location is present, it will be added automatically.
- Direct data transfer must be enabled for downloading directly to the CLC Server's CLC_References File System Location. If not enabled, data can be downloaded to a CLC Genomics Workbench's CLC_References location and then
copied to the CLC Server location using functionality in the Reference Data Manager.
- To work with this location via the CLC Genomics Workbench Reference Data Manager, the Workbench must itself have a CLC_References location. This location is added by default when the CLC Genomics Workbench is installed.