I’m tracking my experiences with Taverna as I prepare to teach a graduate lab class in Bioinformatics Pipeline Programming this summer.
I started off with the most basic of the basic tutorials. Building this masterpiece:
To do this I had to follow four steps.
- Search for “fasta” in the query box directly above the service panel. Choose “Get Protein FASTA” from the resulting NCBI services and drag it to the workflow window.
- In the top menu (Apple menu bar) from the Insert menu, choose “Insert Workflow Input Port”.
- In the top menu (Apple menu bar) from the Insert menu, choose “Insert Workflow Output Port”.
- Drag from the input port to the FASTA service to create an arrow connector, then drag from the FASTA service to the output port to create a second connector. Obviously the arrows should go in the direction you want the workflow to run.
Minor annoyance: I’m old and my eyes are bad. Can I make the text in the workflow window larger? Let’s find out. (It appears after some poking around the menus that I can zoom in on my workflow, but I can’t have bigger text without zooming the whole thing. Moving on.)
Then I ran my workflow by clicking the green “Play” arrow in the Taverna Workbench window menu. A pop-up ensued:
Once I entered a protein identifier (P15409), I could run the workflow. Interaction note, you have to click “Set Value” before you can type anything, the input panes will not activate just with a click.
Results are splendid:
Of course, what I would like to know at this point is “how do I get a whole honking enormous file of protein IDs downloaded” but that is not in fact where this tutorial is going.
We click back to the “Design” view in the Taverna window, and try to add a new service. The service we’re going to be adding is a Soapnet service, located at at http://wsembnet.vital-it.ch/soaplab2/services. Error messages during import, but when we search for the pscan service, it’s there. Drag it over into the workflow window.
Connecting this service is more complicated than the last one because it has multiple input ports. You need to select the “Display All Service Ports” button at the top of the Workflow pane and then connect the output of your sequence service to a specific input port, rather than just to the service as a whole. That looks like this:
The instructions for modifying your workflow also miss one key point — you need to select and delete your old workflow output before adding the new one, or the workflow will hang.
Next time? Using REST services.