[galaxy-dev] Tool-shed - bowtie and tophat dependency

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? -- Thanks, Shantanu