Hi Peter,

> "The short answer is that as of 17.01, Galaxy should install Conda
> the first time it starts up and be configured to use it by default."

yes, it installs everything with conda. So that should work, but I could
also set it up my self manually.

> You didn't confirm which Ballgown you were trying to use in
> Galaxy. Is it this version from Theo Collard:
> https://toolshed.g2.bx.psu.edu/view/theo.collard/ballgown_wrapper/05977e96375b
> If so, this appears to be where he develops it on GitHub, you
> could file an issue there:

and yes that is the version I'm trying to install.

> https://github.com/CollardT/Ballgown-Wrapper

I can contact report the issue on github. It looks like its looking for
a variable called dataset with is not defined in the input part.

this looks like python code?:

## This function returns the name of the sample associated to a given file
#def get_sample_name($dataset, $sample_mapping):
    ##If the file with samples mapping was provided
    #if $sample_mapping != None:
        #return $sample_mapping.get($dataset.name, None)
    ##Otherwise with extract the sample name from the filename
        #return str($dataset.element_identifier)
    #end if
#end def

Cheers Jochen
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