Configuring export from the CLC Server for an external application
The first step when running an external application is the export of data from the CLC Server to the system the software is running on. Starting with CLC Genomics Server 10.0, export parameters can be configured.
Click on the button labeled Edit parameters beside the relevant export. In figure 12.2, the "Sequence to copy" parameter will be exported in fasta format. Clicking on the Edit parameters button leads to a window opening, as shown in figure 12.3.
Figure 12.3: The parameters for exporters are configured in a window like the one shown. Here, the Edit parameter button for the "Sequence to copy" parameter has been clicked. All the parameters here have a locked symbol beside them, so none of them will be offered to the end user to view or change.
Parameters can be configured by:
- Changing the values of default fields. To edit fields that are locked by default, click on the symbol of the lock image to open the lock, then make changes.
- Choosing the parameters to be visible and editable by end users when they run the tool. A parameter with an unlocked symbol beside it will be shown to the end user and will be editable by them. Locked parameters will not be shown and cannot be changed by end users.
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.
Tips for configuring export parameters:
- The parameters listed in the configuration window are all those available for the exporter. Unlocking all of these can result in a confusing, and sometimes conflicting, set of options for end users. We recommend that for parameters that are locked by default, you unlock only those you know to be of interest to your users.
- 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.