Investigated and found the code on how to make folders, changed the code in UCSC Rest as well to make the folders. Nowlan Freese Need your input on on how to organise the folders. Is it okay if I do folders for all the file types or do you want me to make folders for only the few file types that have a lot of tracks. Please review the below screenshot.

I would lean towards putting all files in folders for their file type. As for naming the folders, I would stick with what the API is returning or the naming format here: https://genome.ucsc.edu/FAQ/FAQformat.html

As discussed with Nowlan Freese, keeping the folders for all the file types and naming them according to the track type names returned by the API. Code changes are done and available at https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3689. Please review and let me know if there are any issues.

To test:

1. Download https://bitbucket.org/jaya-sravani/integrated-genome-browser/downloads/ installer or clone this branch to local https://bitbucket.org/jaya-sravani/integrated-genome-browser/branch/IGBF-3689 and start the application.
2. Select a particular genome.
3. See whether UCSC (Rest) datasets are visible inside file type folders (like shown in below screenshot) in the Available data panel.
   

Tested Sravani's branch on my Mac.

Available files appear in their respective folders. Able to load data from each folder. No issues in log when building or running.

Ready for pull request.

Here is the raised pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/999

Merged