> The bug manifests itself when running the tool with "use Defaults" selected 
> results in the following error:
> cp: cannot stat 
> `/data/galaxy-dev/galaxy-dev/database/job_working_directory/000/281/tophat_out/fusions.out':
>  No such file or directory
> 
> It seems that somehow, the filter on the output dataset is not working 
> properly when the value (params['fusion_search']['do_search']) is not 
> explicitly set in the parameters.

Fixed in -central changeset 05a172868303

> The second issue is more minor. It seems that the Tophat2 wrapper assumes 
> that Tophat2 will use Bowtie2 (and not Bowtie).  However, the actual Tophat2 
> program will only use Bowtie2 if it is found in the path.  Otherwise it 
> defaults to using bowtie which results in an error (Could not find Bowtie 
> index files) since the wrapper points the tool to the bowtie2 index instead. 
> To make things a bit more robust, I suggest adding bowtie2 as a requirement 
> to the tophat2 wrapper.  It also might be a good idea to add versions to 
> those requirements.  I've attached a small patch to do that (though it's 
> fairly trivial).

I added the requirements tags for additional packages required by Tophat2; I've 
left out the version information for now because it's fairly brittle. FYI, due 
to limitations with Galaxy's location/index files, the Tophat2 wrapper will run 
with either Bowtie or Bowtie2 but not both.

Best,
J.
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