Editing external applications

Creating and editing external applications is done in an editor like that shown in figure 12.3. To open the editor, log into the CLC Server web client as an administrative user, open the External Applications tab, and then either double click on an existing external application or click on the New configuration... button.

Image extaptsimpleconfig1
Figure 12.3: Different aspects of an external application are configured under each tab of the editor. The External command tab, open here, is where the command to run and its parameters are entered and configured.

An overview of the type of information configured under each of the external application editor tabs is provided below, along with links to more detailed information:

External command:
The name of an external application, as seen by end users, the command line including its parameters, further configuration of parameters with names within curly brackets. Configuring the external command
High-throughput sequencing import / Post-processing
Where relevant to the external application, configuratoin of NGS importer or other CLC post-processing tools that should act on the results of the command line application. High throughput sequencing importers and post processing tools
Stream handling
The handling of standard out and standard error for the command line application. Stream handling
Environment variables that should be present for the external application when it executes. Environment
End user interface
Settings affecting how an external application is displayed in a CLC Workbench client. End user interface
Settings relating to the status of the external application (draft or installed) and other management tasks. Management