I’m tracking my experiences with Taverna as I prepare to teach a graduate lab class in Bioinformatics Pipeline Programming this summer.

Install

Installing Taverna 2.4 on a Mac is simple. First install Graphviz; it is available in *.pkg format so this is trivial. Then install Taverna 2.4. It is available in *.dmg format. Open the DMG file, move the application into your Applications folder, and you’re done.

What I had to do to make it work

When I ran the application I had two errors.

1. The first was a pop-up window telling me that the location of BioCatalogue had moved and that I needed to go here for instructions on how to fix it.

To fix this problem quickly, I went to the top menu bar chose Taverna and then Preferences. I opened up the Service Catalogue menu in Preferences and changed the base URL to https://www.biocatalogue.org (it was http://www.biocatalogue.org).

Fixing this error spawned a third pop-up which I’ll discuss below.

2. The second error was a big red error message in the workflow window telling me that I needed to install “dot”. I suspected this was probably part of the GraphViz package and that it hadn’t installed in the place where Taverna was looking for it. I opened up a shell window and typed “which dot”. Which showed me that I did indeed have a program called dot in /usr/local/bin.

To fix this problem quickly, I went to the top menu bar chose Taverna and then Preferences. I opened up the Workbench menu in Preferences and typed in the complete path /usr/local/bin/dot.

Note: I checked my system file /etc/paths, and /usr/local/bin is already one of the default system paths, so this problem is not with my default system setup. Nevertheless, it’s fixed now, but I file it in the back of my brain in case Taverna has future problems finding other programs that it needs.

After making these changes I needed to restart Taverna for them to take effect.

3. The third error (spawned when I fixed the first error) was a pop-up telling me that I needed to install the Java Cryptography Extension (JCE) and that if I did not already have Java 6 I would have to install that too. I clicked OK. I was prompted to create a Master Password, and I did.

Now it looks like I’m ready to run.