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galaxyproject / ephemeris

Library for managing Galaxy plugins - tools, index data, and workflows.
https://ephemeris.readthedocs.org/
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shed-tools uninstall? #83

Open alexlenail opened 6 years ago

alexlenail commented 6 years ago

Shouldn't it be possible to uninstall a tool?

rhpvorderman commented 6 years ago

This feature is not available in the galaxy API yet: https://bioblend.readthedocs.io/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.toolshed. Only install_repository_revision is there. Not uninstall_repository_revison. So it cannot yet be implemented in ephemeris. Please file a bug at galaxy main to request this feature be included in the galaxy api. Does this answer your question?

alexlenail commented 6 years ago

@rhpvorderman probably galaxy has an API endpoint to uninstall tools because its possible to uninstall tools in the galaxy UI, don't you think? You link to bioblend, so you think I should file an issue on bioblend instead?

mvdbeek commented 6 years ago

Uninstall is using the old controller endpoint, this doesn't have a proper API yet. It hasn't really been a priority up to now since uninstalling is rarely needed, breaks reproducibility for existing analyses and is quickly done without an API. We'll work on this soon-ish I guess.

mvdbeek commented 6 years ago

Contrary to my memory we do actually have the uninstall_repository API endpoint in galaxy. We need to add this to bioblend. ... whcih is a bioblend issue.

mvdbeek commented 6 years ago

Should've really remembered this, since I added it https://github.com/galaxyproject/galaxy/commit/67c66861c50f02475e497aa0c4feec7dfa16c2c2 :D.

alexlenail commented 6 years ago

@mvdbeek I thought I had opened an issue on bioblend but I must have imagined it..

hexylena commented 5 years ago

I'd like this feature, pursuant to the recent fastqc issue we've decided to uninstall some versions, this would be useful there.

hexylena commented 5 years ago

xref galaxyproject/bioblend#285

hexylena commented 4 years ago

The function is now in bioblend if anyone wants to add it here galaxyproject/bioblend#285