GEMINI load 0.18.1.0 fails for missing yml configuration file and database index

[jennaj]

ORG was recently updated to v 0.18.1.0. It needs to have the updated 2018 annotation indexes added. Choosing either 2014/2015 or 2016 annotation causes failures.

Workaround for users: Use the tool at https://usegalaxy.eu. It will fail at https://usegalaxy.org.

Current list of tasks: https://github.com/galaxyproject/usegalaxy-playbook/projects/2#card-15351010

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OLD, keeping for tracking history

To fix the problem:

• [x] Finish two honeybee genome indexes. Involves fixing BWA-Mem DM runtime problems.
• [x] Run https://toolshed.g2.bx.psu.edu/view/iuc/data_manager_gemini_database_downloader/172815da3d41 to get the 2018 indexes installed (DM already installed at Test DM server)
• [x] Test indexes "On test server" ~~- [ ] Update all current DMs~~ ~~- [ ] Make list of missing DMs and add~~ ~~- [ ] Skip this ~~Cleanup data tables so that only the most current Gemini indexes are listed.~~ If users report problems, inform them to use the most current index by date.~~ ~~- [ ] Retest tool on Test to see if all install/dependency issues are resolved~~
• [x] Cleanup Test duplicates in __dbkeys__ table(s) ~~- [ ] Push the new indexes to CVMFS so they are available at ORG.~~ ~~- [ ] Test indexes "On Main"~~ ~~- [ ] Skip this: Consider updating Gemini wrapper so that it better handles what databases to list. It seems like the tool version 0.18.1.0 is dependent on a specific version of the annotation created by the updated data manager version 0.18.1.0. If this is expected ongoing (tool and index version dependent on eachother) -- should the DM should remove all prior indexes and replace with the new one?~~ ~~- [ ] Simplify this ~~Next time we update Gemini, updating the DM and creating indexes should be part of the install process.~~ When the tool is updated, ping to have the existing "most current" index tested and if it fails, create a new one using the matching, newer DM version.~~

The v 0.18.1.0 wrapper fails at both ORG and EU when the 2014/5 or 2016 indexes are selected but they are listed as being available on the tool form. I can't think of another tool that works this way - if an index is listed, it is compatible with the tool wrapper version.

ORG test history: https://usegalaxy.org:/u/jen/h/test-history-gemini

EU test history: https://usegalaxy.eu/u/jenj/h/test-history-gemini-tutorial

ping @davebx @natefoo @bgruening