I'm running KNIME on the server in the console mode only. I belive it is possible to add new nodes (like Math, CDK, RDkit etc) via command line. I can download a zip package of all community supported nodes (via download a zipped update site or Download KNIME Update Site), but where to unzip it then?
I've checked this and some other methods, but finally used the simplest one - installed XFCE4 on the server and then connected via Xming, run KNIME in graphical mode and installed everything is needed. Fast and easy.
The detailed info is here: