On Wed, Mar 30, 2016 at 9:46 PM, Molik, David <dmolik(a)cshl.edu&gt; wrote: Any sample loc files should be provided named tool-data/example.loc.sample and will be copied as example.loc to give default values for the system. This may just mean a section of comment lines with no actual values, or perhaps you can give useful defaults? Here's an example where useful defaults made sense - and these are also used in the tool's functional tests: https://github.com/peterjc/pico_galaxy/blob/master/tool-data/effectiveT3.... https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 If you want to write functional tests using test entries in the example.loc file (i.e. entries not in the default values provided in your example.loc.sample file), use tests-data/example.loc instead and the special value ${__HERE__} to take case of giving a full path. e.g. sample file with no real entries: https://github.com/peterjc/galaxy_blast/tree/master/tool-data/blastdb_p.l... vs. test file pointing at some test entries: https://github.com/peterjc/galaxy_blast/tree/master/test-data/blastdb_p.loc I'm not sure if this last part has made it into the official documentation yet... Can you be a bit more precise? Probably the answer is tool_dependencies.xml etc, e.g. https://wiki.galaxyproject.org/ToolsWithDependenciesInSeparateRepositories Peter