Re: [galaxy-dev] Specifying a PATH for local binaries?

Thanks for the clarification.

However, for my non-interpretor tools Galaxy seems to be ignoring my $PATH (set in ~/.bash_profile). My jobs run on the cluster via SGE so is this likely to be a Galaxy issue or SGE?

Chances are it's SGE. You may want to double check what $PATH is in SGE by running a few test jobs.