On Wed, Mar 30, 2016 at 9:46 PM, Molik, David <dmo...@cshl.edu> wrote: > We're uploading a tool to the Galaxy Toolshed and were wondering about sample > files: > > Should .loc.sample files refer to sample data ( test-data ) > or should they be generalized for integration into other instances of Galaxy?
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.loc.sample 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.loc.sample 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... > Also, how should dependencies be noted? > Can you be a bit more precise? Probably the answer is tool_dependencies.xml etc, e.g. https://wiki.galaxyproject.org/ToolsWithDependenciesInSeparateRepositories Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
