interval2maf remove from unversioned or deprecate

[bernt-matthias]

In order to make the IUC version of the tool work (https://github.com/galaxyproject/tools-iuc/pull/4769) we need to

• remove it from the list of unversioned tools (b7ad595b7298729924a0744fba62ba7a6198410a)
• or just deprecate it (214d11c9214fc9a888db11bfc9aa186855a42fa4)

Intuitively I would suggest the later option since it is know to be broken and we have a working version at IUC (https://github.com/galaxyproject/tools-iuc/pull/4769 will be working after accepting this PR)

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• [ ] I've included appropriate automated tests.
• [ ] This is a refactoring of components with existing test coverage.
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[mvdbeek]

Can you go with https://github.com/galaxyproject/galaxy/commit/b7ad595b7298729924a0744fba62ba7a6198410a ? I'm not sure it's wise to remove tools, just for the potential loss of tool state.

[nsoranzo]

If we don't remove it, maybe at least move it to a deprecated/ subdirectory of tools, and remove it from the lib/galaxy/config/sample/tool_conf.xml.sample ? So people won't try to update it or add it to new Galaxy installations.

[bernt-matthias]

Can you go with b7ad595 ? I'm not sure it's wise to remove tools, just for the potential loss of tool state.

Will do. How about a comment in the tool: stating that no more updates should be done?

[nsoranzo]

Can you go with b7ad595 ? I'm not sure it's wise to remove tools, just for the potential loss of tool state.

Will do. How about a comment in the tool: stating that no more updates should be done?

What about my suggestion? https://github.com/galaxyproject/galaxy/pull/14573#issuecomment-1253445618

[mvdbeek]

I think that if you've had the tool installed (and you've run it at least once) you should keep it installed, so moving the location is also going to break any tool_conf.xml that pointed at the original location.

It's tricky ... if the IUC tool didn't change any of the parameter names maybe it does make sense to drop the file. I'll leave that decision up to you.

[bernt-matthias]

Btw. what exactly is "tool state"?

[nsoranzo]

I think that if you've had the tool installed (and you've run it at least once) you should keep it installed, so moving the location is also going to break any tool_conf.xml that pointed at the original location.

Ah, you're right, should have thought about that! So I guess we are left with:

• From the second commit, keep only the changes to lib/galaxy/config/sample/tool_conf.xml.sample and lib/galaxy/tool_util/xsd/galaxy.xsd
• Add a comment to tools/maf/interval2maf.xml stating that the tool is deprecated in favour of the tools-iuc one.

Btw. what exactly is "tool state"?

I guess Marius means the ability to re-run/inspect the metadata of old output datasets of this tool, plus not breaking old workflows.

[bernt-matthias]

Thanks for the precise suggestions @nsoranzo

[github-actions[bot]]

This PR was merged without a "kind/" label, please correct.