Current UCSC DAS genomes: https://genome.ucsc.edu/cgi-bin/das/dsn
Current UCSC API genomes: https://api.genome.ucsc.edu/list/ucscGenomes

I compared the two endpoints and they do return the same genomes (as of May 14, 2021).

The files that deal with creating and comparing synonyms can be found here in Bitbucket.

These files are located in the Core - Synonym Lookup.

There is a test file for testing synonym lookup: SynonymLookupTest.java that can be found in Core - Synonym Lookup > Test Packages

We may need to double-check that this file is fully testing the example synonyms file. I found an issue where a line in the synonyms.txt that had no synonym (it just contained the IGB friendly name - T_parvula_May_2012) was blocking genomes/synonyms located physically below it in the file from being added to the thesaurus of synonyms in IGB.

Here are the links to the synonyms.txt and species.txt documentation I could find in the IGB User's Guide:

https://wiki.transvar.org/display/igbman/Use+synonyms.txt+to+link+genome+version+names+to+each+other
https://wiki.transvar.org/display/igbman/Personal+Synonyms
https://wiki.transvar.org/display/lorainelab/How+to+add+a+new+synonym+to+IGB

Notes on SARS-CoV-2
https://pubmed.ncbi.nlm.nih.gov/32123347/
https://pubmed.ncbi.nlm.nih.gov/32344679/

Notes on ebola virus
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074192/

I have pushed changes to my branch for review: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-781

To test:
Download branch installer and run IGB
In IGB, navigate to File > Preferences... and then select the Data Sources tab
Check that the IGB Quickload and UCSC data sources are active
In IGB, scroll through the Species dropdown menu in the Current Genome tab.
Check that each of the species names are not abbreviated (for example Enhydra lutris nereis instead of enhLutNer)

Two commits:
I manually added or updated new UCSC genomes. If a species was not found in IGB it was added to species.txt. If a species was already in IGB but had a new genome version that was not present, the new genome version was added to the synonyms.txt.

There were two edge cases where the synonyms.txt was not behaving as expected. This was due to the UCSC_REGEX pattern in SpeciesSynonymsLookupImpl.java assuming that the UCSC keys were a max of 6 letters and 1 number. However the UCSC keys for Cricetulus griseus (criGriChoV) and Enhydra lutris nereis (enhLutNer) are longer. I updated the regex to accept up to 10 characters and a number, though this assumption may eventually break as well.

I have created IGBF-2861 to investigate another edge case that was identified. In order to add the opossum genome (M_domestica) I needed to add a variety to the end (M_domestica_metatherian) to keep it distinct from M_domestica_Borkh.

Testing of the IGB Genomes (genome dashboard)
The genome dashboard accesses the species.txt and synonyms.txt files from bitbucket (see here), as well as the quickloads that are specified in the igbDefaultPrefs.json file on bitbucket.

We will need to conduct post-merge testing to determine how the genome dashboard behaves with genomes that are only provided by UCSC DAS, of which there are now many. There could be complications if the UCSC DAS data source is disabled by default, as clicking on a genome provided only by UCSC DAS in the genome dashboard would be unable to load in IGB.

Tested the branch installer mentioned by Dr. Nowlan Freese. The species names aren't abbreviated. They are in their complete name.

Dr. Nowlan Freese, you can go ahead and submit the pull request.

Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/879/igbf-781

Modifying bioviz-playbooks "replace" role to edit genome dashboard util.js file during deployment to also use user-specified IGB repository and branch.

Deployed genome dashboard to bioviztest.bioviz.org using the proposed fork and branch. Confirmed that utils.js contains the following variables:

const SPECIES = 'https://bitbucket.org/nfreese/nowlanfork-igb/IGBF-781/core/synonym-lookup/src/main/resources/species.txt';
const SYNONYMS = 'https://bitbucket.org/nfreese/nowlanfork-igb/raw/IGBF-781/core/synonym-lookup/src/main/resources/synonyms.txt';
const ALLQUICKLOADS = 'https://bitbucket.org/nfreese/nowlanfork-igb/raw/IGBF-781/core/igb-preferences/src/main/resources/igbDefaultPrefs.json';

I see no difference between the genome dashboard deployed above and the version deployed on bioviz.org (main site). The only thing that looks a bit weird is that both sites don't have a picture for genome F_albicollis_Jun_2013 (collared flycatcher). This was added recently to IGB Quickload svn repository, and we (mainly me) forgot to add a photo to the genome dashboard repository. This has nothing to do with the current issue however.

Based on the above review, I think it is fine to now merge the pull request.

Merged and built master branch installers. Ready for testing.

Tested on Mac master installer.

Working correctly.

Tested on Windows and Linux. The species names aren't abbreviated. They are in their complete name.

Closing the issue.