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 env.sh 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 env.sh and it worked perfectly.
This document explains how the default symlink and env.sh are used by Galaxy:
Thanks for any suggestions.