gops subtract broken

[dannon]

The latest release of the gops subtract tool available in the toolshed doesn't work because of missing utils dependencies. The older version installed by suite_gops does work, however.

It's just a guess, but I'm thinking improper handling of the symlinks added in a36d751 is what caused this -- that whatever process packages the tool from the tools-devteam repo and pushes it to the toolshed ignored the symlink.

Reported by @lparsons

[dannon]

(debugging discussion from IRC available at https://botbot.me/freenode/galaxyproject/2016-02-09/?msg=59708461&page=3)

[nsoranzo]

It seems that the Planemo upload of https://toolshed.g2.bx.psu.edu/view/devteam/subtract/ecb36112b056 correctly transformed GitHub symlinked files in real files, while it did not work for the tool_collections/gops/subtract/utils -> ../flanking_features/utils/ directory symlink.

Ping @jmchilton.

[martenson]

@nsoranzo planemo does not populate symlinked folders

[nsoranzo]

@martenson What about galaxyproject/planemo#29 ?

[davebx]

@nsoranzo If memory serves, that only applied to the --tar_only flag.