Data on the server

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

Referring to data in a CLC Genomics Server data area:

For data already available within the CLC Genomics Server, the beginning of the URL will always be:

clc://server

For the rest of the URL, there are two main choices in how to provide the location of the data object:

Please note that there is a third form of URL that can be used. This alternate form includes the machine address and port that the Genomics Server is running on as part of the initial section of the URL. An example of this URL form would be:

clc://server.com:7777/server_data/project1/sample1.

Since you provide server and port information as part of clcserver command anyway, this form of URL is generally not necessary.

Referring data to be imported into the CLC Server:

Data files residing on the same machine as the CLC Server but not yet imported would usually also be referred to using CLC URLs. 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.

CLC URLs specifying the file (in an Import/Export area) containing the data start with clc://serverfile/ . The rest of the URL should give the full path to the file (from the root of the system it is stored on). For example:

clc://serverfile/mnt/data/project1/s_1_1.sequence.txt

The clc://serverfile/ part of the URL indicates that the file being referred to is in an Import/Export area configured for the CLC Server. The full path to the file to be accessed is /mnt/data/project1/s\_1\_1.sequence.txt .

Data to be imported may also be stored on the local system, where the clcserver command is being run from. In this case you would just use a path to the file directly and would not need to use a CLC URL 2.1.

Note: Please do 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".

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.



Footnotes

... URL2.1
Running the clcserver command on the same machine the CLC Server sofware is installed on is unusual, but if you have chosen to do this, you can of course import data from anywhere on that system that you, as the user logged into the server machine, have access to. For this you would then need to provide local file system locations. Alternatively, you could instead provide CLC URLs indicating an Import/Export area of the CLC Server, just as you would when running the clcserver command from a different machine.