> I'm confused.  So I installed tophat-2.0.6.Linux_x86_64 which seems to
> contain tophat and tophat2.  

tophat2 redirects to tophat, which is tophat version 2.X.X

> Can't galaxy use that tophat?

You can, but you need to use the Tophat2 wrapper, not the Tophat for Illumina 
wrapper. And, when you use the Tophat2 wrapper, you'll need to have Bowtie2 
installed and the bowtie2_indices.loc set up appropriately.

J.
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