WIP Modernize RGI tool and data manager

[bernt-matthias]

Tool was requested by one of my users - but needs a few improvements which I plan to contribute here. Ping @raphenya, @agmcarthur, @innovate-invent, @arpcard

Starting this PR as work in progress:

• add IUC style github workflows (only requires to set TS_API_KEY and TTS_API_KEY)
  • this will properly deploy tool and datamanager (DM is not yet deployed)
• restructure repo a bit
  • data manager is now here (https://github.com/arpcard/rgi_database_builder could be archived)

Will continue here:

• datamanager should download versioned data
• to should not make use of __tool_data_path__ but use the paths defined in the data table
• more tests needed

Also:

• add to planemo monitor (to get containers for the data manager - the tool should already have one, because it uses only a single bioconda requirement)

[github-actions]

Stale pull request message

[natefoo]

We've had a request to install this tool on usegalaxy.org, the modernization here would go a long way to making this possible. Any chance this could get a review and merge?

[natefoo]

@bernt-matthias the DM was already moved to this repo, looks like your changes revert some of the modernization that was already done.

[bernt-matthias]

I see. Seems that I was out of my mind.

• I will drop 6950b7f and 08ff569
• Someone should remove https://github.com/arpcard/rgi_database_builder ?

[bernt-matthias]

@raphenya @agmcarthur how should we proceed here? I'm happy to put some more work into this, but I will need a bit of feedback.

[tcollins2011]

I've received more requests to get the RGI wrapper updated and on galaxy main again. Is there anything that I could do to help? There are quite a few people requesting this now.