I've set-up a local Galaxy instance and have been using the data manager / 
tool-shed to set up tools and indexes etc.

I've installed both bowtie2 and tophat2 but when i come to run tophat 2
I get the following error:

tophat2 --num-threads ${GALAXY_SLOTS:-4} 

[2015-07-01 16:22:24] Beginning TopHat run (v2.0.9)
[2015-07-01 16:22:24] Checking for Bowtie
  Bowtie 2 not found, checking for older version..
Error: Bowtie not found on this system.

Clearly there is an issue here with tophat2 knowing where bowtie2 is. What I 
can fathom is where this is assigned and how to get this working.

In my tool_dependency_dir/bowtie2 there are both 2.2.4 and 2.2.5 packages - 
this has confused me a bit, but i think it was because the 2.2.5 is a 
dependency of tophat2 and 2.2.4 a dependency of bowtie2.

Thanks in advance for any insight and help - I suspect it's something trivial 
as i'm quite new to Galaxy.
Simon D. Harding, PhD.
MRC IGMM at University of Edinburgh
Crewe Road, EDINBURGH, EH4 2XU

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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