[galaxy-dev] Getting bowtie2 and tophat2 to work on galaxy on amazon aws cloud

Dear all, I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman distribution (ami-118bfc78). The instatiated Galaxy however does not contain Bowtie2 and Tophat2, even after updating through the Cloudman Admin section. Although the wrappers are there in the tools directory, when I access it through ssh. I've also installed Bowtie2 manually on the server and the command bowtie2 does get recognized. How cat I get these two to run on the Galaxy instance? Thanks for your help. Best Stanislas