Add a script to reorganize tool data based on the new layout for genomic Data Managers

[natefoo]

In #19013 I mentioned that I would write a script to move data from the old layout used by the most common genomic DMs to the new standardized layout - here it is.

Caveat: The __dbkeys__ and twobit tables do not have the dbkey/value(variant) distinction, in these cases the dbkey would be the variant. So in the (rare) case you have a variant in these tables you would need to do some manual post-processing.

DM layout changes were in galaxyproject/tools-iuc#6489

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. Install some data using old versions of data managers
  2. Run python ./scripts/reorganize_tool_data.py --tool-data-path /path/to/data --prune-dirs ./config/tool_data_table_conf.xml
  3. Observe proposed expected changes
  4. Run python ./scripts/reorganize_tool_data.py --tool-data-path /path/to/data --prune-dirs --commit ./config/tool_data_table_conf.xml

I just used this to reorganize the brc.galaxyproject.org CVMFS repo - results can be found at http://datacache.galaxyproject.org/brc/ once publishing is complete and changes propagate.

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[github-actions]

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