Hi Chris,

I am glad that we figured this out. So I am not sure what the best strategy for datatypes with code dependencies is, we should open a new thread or git issue and see if someone can help with that.

Thanks,
Sam

On Wed, Dec 14, 2016 at 10:59 AM, Cristel Thomas <cristel.thomas@gmail.com> wrote:
Hi again,
ok, ran some more tests - we switched to a new dev server recently and we were having the issue because of the R/rpy2 thing. 

With that taken care of though, we still have files in the dropdown that shouldn't be there - no more FCS, but .ypnb still show up. I guess this is because of the implicit conversion?

I would love some input on what you guys think we should do about adding the FCS datatype to Galaxy.
Thanks again,
Cris

On Tue, Dec 13, 2016 at 8:52 PM, Cristel Thomas <cristel.thomas@gmail.com> wrote:
Hey Sam,
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

On Tue, Dec 13, 2016 at 1:24 PM, Aysam Guerler <aysam.guerler@gmail.com> wrote:
Hey Cris,

Dannon and I figured out, that the problem is that your datatypes are not loaded properly, due to these two invalid imports: 


Removing them fixes the issue. The error for this is shown in the server log.

Thanks,
Sam