Connecting to a CLC Server

The CLC Server Connection dialog in CLC Workbenches can be used to log into or out of a CLC Server, as well as check on the status of a server connection. It is launched from the menu system by going to6.1:

        File | CLC Server Connection (Image server_16_n_p)

The location and port of CLC Servers that Workbenches are able to connect to can be pre-configured for all users of a Workbench on a given machine by placing a file called into the settings folder under the Workbench installation directory.

A file contains two lines for each CLC Server that should be listed in the drop down list within the CLC Server connection dialog in the Workbench.

For example, if 2 servers are available, the file would take the following form: = <hostname>
server.1.port = <portnumber> = <hostname>
server.2.port = <portnumber>
where <hostname> should be replaced with the name of the system the CLC Server is running on and <portnumber> by the port number of the CLC Server, typically 7777. The numbers in the parameter names (e.g. server.1.x, server.2.x) are used to specify the order the servers are presented in the dropdown list presented to users connecting from the Workbench. The order of the lines themselves does not matter. Up to 8 servers can be listed.

You can download an example file at

If a file is present under the settings folder of the Workbench installation, the name of the CLC Server entered for the parameter in the file, and its port number, are initially presented in the dialog for all users of the Workbench on that system. When multiple servers are available, users can just select the one they want from the drop down list.

Machine level and user level CLC Server settings

To log into a CLC Server, Workbench users need to supply the CLC Server name and port, as well as a username and password. The server name, port and username will be remembered between Workbench sessions. This information is saved in their user settings file, usersettings.xml, whether or not a file exists.

Users can specify if they want their password to be stored. If they do, the encrypted password is saved in the usersettings.xml file. If they choose to save their password, they will also be able to specify if they want the Workbench to log into the CLC Server automatically each time the Workbench starts up.

If server information is present in both a user's usersettings.xml file and the central file, then the information from both is presented in the CLC Server Connection drop down list of servers. If the server information is identical in both files, only one item will be listed per server. If there is more than one server, the order they appear in the drop down list is determined by the information in the file.

Further details about the file

Only servers for which there is complete information (both a host and port setting) are presented in the CLC Server Connection drop down list of servers. If incomplete information is found in the file, (e.g. a host name setting with no corresponding port setting or vice versa), an error will be written to the CLC Workbench log file (clc-workbench.log), but any complete entries found in the property file will still be listed.

After a file is in place, server entries can be added or removed by directly editing the file.

Server details can also be added to indirectly: if the configured servers were read from the file and a user successfully logs into a CLC Server, and that user has write permission for the properties file, the server name and port used when logging in will be written back to the file as the first server in the list. I.e. that server's details will be entered as the, and server.1.port settings, with other servers' details moved down in priority. This server will then be the first one listed in the drop down list in the CLC Server Connection dialog for all users of the Workbench on that system.

The format of the files for CLC Genomics Workbench 11.x and earlier, CLC Main Workbench 8.0.x and earlier, and all versions of Biomedical Genomics Workbench software was different to the format described above. For those software versions, only a single server was supported. An example file for those versions can be found at


... to6.1
The CLC Server Connection option was introduced in CLC Genomics Workbench 12.0 and CLC Main Workbench 8.1. For connecting to a CLC Server using earlier versions of these programs, or the Biomedical Genomics Workbench, the CLC Workbench Client Plugin needs to be installed. This can be found in the Workbench Plugin Manager of relevant software versions.