Running Velvet from the Workbench

Next step is to test if it can actually be executed. Open the Workbench with the External Applications Client Plugin installed. Go to:

        Toolbox | External Applications (Image server_location_closed_16_n_p) | CLC bio Velvet (Image externalapplications)

When you have selected the execution environment the parameters must be configured in the dialog seen in figure 8.16.

Image external_app_configure_parameters_velvet
Figure 8.16: Configure Velvet parameters from the Workbench.

Select (Image browse) some sequences, adjust the parameters accordingly and click Next and Finish.

The process that follows has four steps:

  1. The sequencing reads are exported by the server to a FASTA file. The FASTA file is a temporary file that will be deleted when the process is done.
  2. The velvet script is executed using this FASTA file and the user-specified parameters as input.
  3. The resulting output file is imported into the save location specified in the save step of the Workbench dialog, and the user is notified that the process is done.
  4. All temporary files are deleted