Scripting:

https://wiki.transvar.org/display/igbman/Scripting+and+the+IGB+command+language
https://wiki.transvar.org/pages/viewpageattachments.action?pageId=17269487
https://gist.github.com/Hillrunner2008/25976458488b65a3a25b

Fixed the issue. Need testing with Linux and Mac OS.
https://bitbucket.org/ashwiniK27/integrated-genome-browser/commits/f444a6118b9b6b92f05e7e4c0d48e1eb3d7a3911?at=IGBF-1182

Removed '.js' from file chooser UI as 'Run Scrpt' does not support javascript files.

First Level Review :
Bug is fixed on macOS. 'Run Script' is working as expected. Only .igb files are selectable by user. No support for javascript file as specified in fix.
I did not do code-review as I have written it and expect that such review should be done by other developer.

Working on Mac and windows. However not working for Linux. Adding back to do List. Please see attached imaged.
Code review done for fix which is working on windows and mac. Need to do it again once the fix for linux is added.

Dr. Loraine suggested that if you are building code from command line/terminal, change may not be reflected with latest jar.

Sanket, could you please test the issue again by building the jar from netbeans instead of command line? Because I noticed that image you attached with issue for reference is not showing latest code change. (File chooser window should have 'Choose File' as title instead of 'Open). It is possible that you are not working with modified code.
Please let me know the outcomes of new build on Linux.

Moving to 'Needs 1st level review'.

Good catch Ashwini. I will test it again on Linux.

As pointed out by Ashwini, i tested a jar build using netbeans. Its working fine on linux as well. Attached screen shot.
As mentioned in earlier comment code review is done.
Moving this issue to Ready for pull request.

Submitted Pull Request

After testing this story I can confirm that the Tools menu's "Run Script" file chooser has been changed to the operating system's native file chooser. This has been tested on Mac and Windows and is functioning as expected. Scripts are still operating as expected and there seem to be no side effects resulting from this change. Since this issue is resolved it will now be closed.