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.tho...@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.guer...@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:
>>
>> https://github.com/ImmPortDB/immport-galaxy/blob/release_16.
>> 07/lib/galaxy/datatypes/flow.py#L13
>>
>> Removing them fixes the issue. The error for this is shown in the server
>> log.
>>
>> Thanks,
>> Sam
>>
>
>
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