Can confirm, things look good! The name is showing up in the data access file on the master installer. If there are no objections, I'm moving to closed.

Merged. Master branch installers are built. Ready for testing.

Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/877/igbf-2848-get-name-of-refseq-file

1st-level review: Can confirm, the correct file .2bit file name for A_thaliana_Jun_2009 is showing up when I use Dr. Freese's branch installers. The code change itself looks good too! Recommending pull request.

OK thank you for the explanation! In that case, the new change is fine.

The sequence data file has shown up under available data since at least 2015. Sequence files are handled differently with custom genomes and it may require significant changes in logic for the sequence file to not be displayed under available data. We could create a new ticket for removing the sequence file from available data and include it as part of 9.1.10.

Should the sequence data file be listed under "available data"? Note that the "available data" section lets users add and remove data sets from tracks by clicking the boxes. There is logic there that might not interact well with reference sequence data.

Issue was that fileName variable was not being set in NewGenomeAction.java

Commit: https://bitbucket.org/nfreese/nowlanfork-igb/commits/3c32f05bba8da598fb6d256a2f0bbb0ce9f1d3df?at=IGBF-2848

To test:
Download my branch installer for IGBF-2848
Install and open IGB
Select File > Open Genome from File...
In the Reference Sequence box paste this url: http://igbquickload.org/quickload/A_thaliana_Jun_2009/A_thaliana_Jun_2009.2bit
Click OK
Select the Data Access tab and look at the Available Data box.
Under Local Files the name A_thaliana_Jun_2009.2bit should appear.