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 | CLC Server (Image server_16_n_p) | External Applications (Image externalapplications)

You will now see a list of all the applications that have been set up (figure 8.11).

Image clustal_workbench
Figure 8.11: Running Velvet from the Workbench.

In this case there is only one. When you click Next, you can select (Image browse) some sequences, set a few parameters 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