We have migrated bowtie tool wrapper from dist to tool-shed using migration 
script # 7 with install_dependencies option. We removed our locally installed 
bowtie binaries so that install_dependencies option would work fine. I think an 
earlier release would skip dependency installation if they were found in PATH. 
The tool-shed installed bowtie is working fine, however, dist included tophat 
is broken now as it is failing to find bowtie binaries. Should we install back 
bowtie outside of tool-shed OR is there a tophat wrapper that can handle this 
dependency? Any pointers?

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