On Wed, Mar 30, 2016 at 9:46 PM, Molik, David <dmolik(a)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....
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...
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