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I have add an init script now. I have already placed a copy in /etc/init.d but it is pointing to stuff that won't exist until you merge this branch in. So after you have done that you should execute: "/etc/init.d/eiSearchServer start" to start the server. The errors you were getting were caused by the wrong version of eiR being installed, namely, I had installed a development version that worked with the server, but at some point the latest bioc version got installed on top of it. I will have the version that works merged into bioc either today or tomorrow so it should not be a problem again.