General configuration of external applications

Here, we describe the configuration of an external application that uses the system cp command to create a copy of the sequence data that a user selects. This is an artificial, but simple example, allowing us to explain many aspects of external application configuration using a command we expect will be on server systems.

Figure 12.2 shows a configuration for the cp external application. It is named "Copy sequence data", and would result the data selected by a user being exported from the CLC Genomics Server in fasta format, copied, and then the copied file being imported back into the CLC Genomics Server.

Overview of configuration steps

  1. Log into the web administrative interface for the CLC Genomics Server and click on the External applications tab.
  2. Click on the New configuration... button.
  3. Add a name into the External application name field. This is the name of the external application that a user will see via a Workbench or the CLC Server Command Line Tools.
  4. Enter the command to be launched when a user runs the external application into the Command line field. This means the command itself, its parameters and values. Any value that the CLC Server uses, e.g. to define exports or imports, and any values that should be available to a user to configure, must be enclosed by {curly brackets}.

    Each time a set of curly brackets is entered into the Command line field, a corresponding entry is added into the General configuration area. The name of that entry will be the text entered between the brackets. The same name will be presented to end users for the values they have access to, either as a parameter label in a Workbench wizard, or as a CLC Server Command Line Tools parameter name.

    Image extaptsimpleconfig1
    Figure 12.2: Setting up the cp command as an external application. Here, two values are specified. The type chosen for the first one results in the end user being prompted to select the data to copy. The type chosen for the second one specifies that the output from the cp command will be in fasta format and should be imported back into the CLC Genomics Server using the appropriate importer.

  5. Configure each parameter using the options offered within the General configuration area.

    All entries in the command line that are enclosed by curly brackets will be substituted at run time by values. The following sections describe how to configure an external application so the relevant information is substituted.