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:
clc://server/server_data/project1/sample1
The above URL starts with clc://server
, indicating that the data in question is stored in a CLC Server data area. In the example here, the data object is held in a CLC Server File Location called server_data
, inside a subfolder called project1
. The data object itself is called sample1
.
Please note the above is a URL pointing to a data object. It is not a path to the file that contains the data object. This means that it would be very unusual to see a data object with a name ending in ".clc". The name for a data object in these URLs is the same as the name presented in the Navigation area when you are logged into your Server from your Workbench.
If a data object's name has spaces or unusual characters in it, you will likely need to escape those characters or include quotes around your data object name in the CLC URL.
clc://server/BAAAAAAPc132--7fff/-268177574-7fff
The above URL agains starts with clc://server
indicating that the data in question is stored in a CLC Server data area. What follows is the ID to refer to the data object.
A big 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
).
One would most commonly get such an ID as part of the scripting process one sets up. Please refer to the Result files and connecting analyses in pipelines section for further details on this.
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".
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.