thanks, I'll check tomorrow at work but I suspect there might be something else - I use rpy2 to call R, so that FCS files can be read. As of 2 months ago there was no efficient way of doing it strictly in python. rpy2 does not load if R isn't installed on the system (and for this specific script, it requires flowCore installed in R).

We have R installed on our instance and still have the issues I described earlier (though I will double check tomorrow and keep you posted). 

In the long run the rpy2 thing might be an issue. We want to add our tools and the datatypes to galaxy. I'm not sure how to get around to doing it without rpy2. I'd like to keep a sniffer function in there.

Thanks again,

Cris