Hello, We recently transitioned from a CloudMan instance of galaxy to our own cluster and started having problems with calls to tools from within other tools. For example when Tophat calls bowtie-inspect its not finding the executable. To fix this I listed bowtie in the requirements section of the tophat wrapper like so: <tool id="tophat" name="Tophat for Illumina" version="1.5.0"> <description>Find splice junctions using RNA-seq data</description> <version_command>tophat --version</version_command> <requirements> <requirement type="package">tophat</requirement> <requirement type='package'>bowtie</requirement> <requirement type="package">samtools</requirement> </requirements> Now I am wondering, is it generally expected that all tools used by galaxy will have their executables on the user galaxy's PATH? Is the above a good solution? Or is there something else likely amiss with our galaxy setup? I think we recently pulled updates for some major tool_shed release but I haven't been able to determine if any of the tools listed above were affected by that. Wish I were in Český Krumlov asking this question. Missed the registration deadline...doh. Thanks, Andrew Warren