HomeCLC FAQ - CLC Genomics Server and Command Line ToolsCLC Genomics ServerWhy can't I specify an Import/Export directory to be a subfolder of a CLC File Location?

2.8. Why can't I specify an Import/Export directory to be a subfolder of a CLC File Location?

The action of setting up an Import/Export location is a means for designating where the CLC Server is allowed read and write access. This is described in the manual page about setting up Import/Export locations:


Import/Export directories should not be located within areas designated as CLC File Locations on the Server.

CLC File Locations for CLC Servers, and CLC Data Locations for CLC Workbenches, should be used for CLC data only. Data should only be added or removed from these locations by CLC software.  This is because CLC File Locations and CLC Data Locations contain indexing and other information about the contents of those folders, which is kept up to date by the software.

By CLC data, we mean data that is imported into the software or has been generated by the software itself.

By definition, an Import/Export folder is intended for holding non-CLC data (with extension different from .clc ). Commonly, this would include:

  • sequencing data that will be imported, such as fastq files
  • data exported from the CLC Server
  • BLAST databases

If your aim was to have all data that had any relevance to your CLC software in one place, then you could create two folders at the same level to do this. For example, you could create a folder called CLCDataRelated. You could then have subfolders:

  1. CLCDataRelated/CLCServerFileLocation
  2. CLCDataRelated/Import-export

Of course, an Import/Export Location does not need to be in any particular place. It may also be that you already have a place where you store sequence data and plan to import from it. You may also have an existing location where you export your data to. As long the owner or administrator of the file system area approves it, then any folder could be designated as an Import/Export area for the Genomics Server, except for an area already designated as a CLC File Location or a subfolder of such an area.

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