Nate Coraor wrote:
Chris Cole wrote:
Finally, and more generally, which paths does Galaxy search for finding tools, if not explicitly set?
I've had a look on the wiki, but I can't find this information. Any help would be appreciated.
Hi Chris,
As you've discovered, tools are expected to be located in the same directory as their xml file if an interpreter is set. If an interpreter isn't set, $PATH is used instead (but the interpreter itself is assumed to be on the $PATH). This allows tools to be installed independently of Galaxy, but for the wrapper scripts within Galaxy to still be locatable.
Hi Nate, 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? Chris