So in my previous post I wanted to do a hypergeometric test in R. Now I want this test to be executed from Taverna (RShell). This means we need to install R as a server. How to do this is explained in detail here. Once installed we need to start Rserve to allow Taverna to connect to it. This is done as follows:
> library(Rserve) > Rserve(args='--no-save')
Note that the args can be ‘save’, ‘no-save’ or ‘vanilla’.
In Taverna an RShell can be added to the workflow to execute an R script. This script can be edited / defined by right-clicking the node and choosing that particular option.
Currently, when running a workflow in Taverna 2.1 beta2 and R 2.9.2 results in a handshake error. Apparently Rserve uses a newer protocol version than Taverna does.