External command

The 3 sections under the External command editor tab, as shown in figure 12.3, are:

External application name
The name that end users see via the CLC Workbench Toolbox menu or use to launch the external application using the CLC Server Command Line Tools.
Command line
The command line to be run, including the full path to the application and its parameters. Parameters and values that will not be configurable by end users are written as normal. Parameters values that should be substituted at run time are written within {curly brackets}. This includes parameters that should be configurable by the end user.
General configuration
Parameter values specified in {curly brackets} in the Command line field have a corresponding entry in the General configuration area. Here, those values are configured, including specifying their type, and for some types, configuring the values to be applied or offered to end users to select.

For illustration, the simple example of the cp (copy) command with 2 positional parameters is shown in figure 12.3. In the General configuration area, the Sequences to copy parameter is set to User-selected input data (CLC data location) meaning that the end user will specify the data to be copied from a CLC File Location. That data will be exported using the fasta format. The Copied sequences parameter is set to type Output file from CL, indicating that this is the output from the command, and the standard fasta importer was selected for importing the results into the CLC Server.

Command parameter value types

Details of parameter value types are outlined below. A brief description is also provided in the web administrative interface when a value type is selected and the mouse cursor is hovered over it. Particularly important types for external application configurations are User-selected input data (CLC data location), which is the usual choice for parameters specifying input data, and Output file from CL, which is the usual choice for specifying results generated by the command line application.

Image extappexportparamconfig
Figure 12.4: Clicking on the Edit parameters button for the "Sequences to copy" parameter brings up a window with the editable parameters for the selected exporter. Parameters with a locked symbol beside them are not shown to, and are thus not configurable by, the end user.

A tip for exploring how many files an exporter will generate

A simple way to explore how many files an exporter will generate with a given configuration is to set up an external application using the echo command and a single parameter linked to the exporter of interest. Set up the Standard out handling to Plain text. This is described in Stream handling. The output from such an external application is a file, which is re-imported into the CLC Server as a text file. This file contains the full paths to the files the exporter created.

If an exporter is configured in a way that will lead to multiple output files, then the full path to each output file will be substituted in the command at runtime. The external application itself must be able to handle the outputs generated.


Configurable export parameters were introduced with CLC Genomics Server 10.0.