Data on the server

For files already on machine housing the CLC Genomics Server, you need to provide the data location as a CLC URL. These start with the text clc://.

Files already uploaded to the CLC Genomics Server data area:

For files already available within the CLC Genomics Server, you have a choice of providing a CLC URL with the (human-readable) path to your file, or providing a CLC URL with an ID that the CLC software understands. The former is easier when working on the command line directly. The latter is used primarily when working with pipelines of operations, for example when scripting.

Examples of providing file locations for data uploaded to the CLC Genomics Server data area include:

The advantage of using IDs over the path to the file is that the ID of the data remains the same, even if the data object is renamed or moved. If you wish to work with data IDs on the command line, you can be easily get these using the Workbench. See figure 2.1. IDs of data locations look something like this: BAAAAAAPc132--7fff/-268177574-7fff. The first part of this example ID gives the data location (BAAAAAAPc132--7fff), and this is followed by the ID for the file (-268177574-7fff).

Files ready for upload to the CLC Genomics Server:

You can also use data files residing on the same machine as the CLC Server, but not yet imported into a CLC Server File Location, for particular functions (e.g. import). Such data needs to be in a location that the Server is allowed to access. Such areas, known as Import/Export directories must be explicitly specified by the CLC Server administrator via the web administration interface.

To use data in one of these areas, the serverfile version of a CLC URL is provided: clc://serverfile. For example:

Note: It is important not to put raw data, or any other non-CLC files, into a directory designated as a CLC Server File Location or any of its subdirectories using standard system tools (e.g. drag and drop, system copy or move commands, etc.). This is because the indexing system used within the CLC Server File locations is very sensitive to unexpected changes, i.e. "non-CLC actions". We highly recommend that any Import/Export directories you configure on your CLC Server are NOT within an area designated as a CLC Server File Location.

Image clc-url-copy
Figure 2.1: Copying a data object in the workbench will put the CLC URL on the clipboard. You can then paste the URL into your command in the terminal.