Running from a CLC Workbench
External applications are executed from the CLC Genomics Workbench by going to:
Toolbox | External Applications (
)
Note that external applications are only synchronized between the server and the workbench during login thus users will have to log out and log in again to discover new external applications.
The configured and accessible external applications are available as individual tools as seen in figure 12.8.
Figure 12.8: Selecting the external application to run.
When the External Applications item is launched, the dialog shown in figure 12.9 is displayed. There are two types of execution environment: The CLC Server environment, and grid presets. The CLC Server environment is always present, while grid presets are only shown if they have been configured as described in Model II: Master server submitting to grid nodes.
Figure 12.9: Selecting execution environment.
In order for an external application to be executable in a grid environment, its working directory must be configured as a shared temp-dir (see Working directory for details).
Clicking Next will display the wizard for providing values for the parameters as can be seen in figure 12.10. Here the in parameter is displayed as a CLC Object selection, as configured in Basic configuration.
Figure 12.10: Providing the parameters to the external application.