"Phantom" tool dependencies when installing from toolshed?

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"Phantom" tool dependencies when installing from toolshed?

Peter Briggs
Hello Galaxians

I've been reinstalling some tools and dependencies as a part of relocating our local Galaxy server to a new VM platform, and while the majority of tools seem to be okay for a few I've noticed a baffling problem with what appear to be "phantom" tool dependencies.

For example: for package_matplotlib_1_2, I'm now seeing an unsatisfied dependency on "package_libpng_1_6_7" from devteam - but the matplotlib repository in the toolshed no longer has a requirement on this package. So I don't know where this phantom dependency has come from (a hangover from the original installation, which was at an earlier revision of the package?) or more pragmatically, how to clear it.

Has anyone else seen this problem before, and if so then can they advise how to fix it?

To clarify:

-- By "reinstall" I mean: manually uninstall the tool repository via the Admin/Manage installed tools interface, and then perform an install using a Python utility that uses the API via bioblend.
-- I'm using Galaxy v15.10.2 but planning to upgrade the code base once the tools are installed.

Any help or advice greatly appreciated,

Best wishes


Peter Briggs [hidden email]
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

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