This may be a problem with the latest Galaxy Cloudman AMI.

Some tools (tophat is one) are failing to run because they cannot be found. I 
have noticed that after launching a new instance with the latest AMI, the 
"<package>/<version>/default" sym-links under /mnt/galaxy/tools point to a 
directory in /mnt/galaxyTools, which does not exist since this new AMI merged 
galaxyTools and galaxyData.

Additionally, even after manually fixing the symlink and the path in the 
file (it also references galaxyTools), running tophat would fail, although now, 
at least, it can find the program. This may be an issue with tophat's XML or 
python script though, since I fixed Velvet's symlink and and it worked 

This document explains how the default symlink and are used by Galaxy:

Thanks for any suggestions.
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