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galaxyproject / tools-devteam

Contains a set of Galaxy Tools mostly written by the Galaxy Team.
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gops subtract broken #333

Open dannon opened 8 years ago

dannon commented 8 years ago

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 a36d7515356531059ef95093577d42422c8f2d13 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 commented 8 years ago

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

nsoranzo commented 8 years ago

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 commented 8 years ago

@nsoranzo planemo does not populate symlinked folders

nsoranzo commented 8 years ago

@martenson What about https://github.com/galaxyproject/planemo/pull/29 ?

davebx commented 8 years ago

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