IGV issues on MacOS Big Sur 11.4

[Leah Wells]

Hi,

Since I have updated my mac to macOS Big Sur 11.4, I am unable to open IGV. I have tried reinstalling and it seems to install but then when I try to open it just either closes or doesn't do anything.

Hoping you can help.

Many Thanks,

Leah

[Helga Thorvaldsdottir]

Hi Leah,

There were issues with IGV today that have been resolved. Can you try again, in case those issues were affecting you.

If it still doesn't work you can try reseting all preferences to the IGV defaults by renaming (or removing) the files prefs.properties in the igv folder in your user home. Do this while IGV is not running, and then restart IGV

If that doesn't help, can you send us the information from the log of the IGV run that fails. The log can be found in the igv.log file under the igv folder in your user home. Also let us know which version of IGV you are running (IGV version number, and also whether you are running the Mac App with or without Java, or the command line version).

Helga

[Leah Wells]

Hi,

I have tried again however the issues are still persisting. 

I am trying to use the desktop MacOS app which is the one with Java attached. The version is IGV_2.9.4. I have also tried without the Java however the same thing happens.  

I don’t have a log file as it is opening the desktop app I am having issues with. As mentioned, it seemed to work before I updated my Mac to Big Sur 11.4 so perhaps it’s something to do with that?

Many Thanks,

Leah

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[Helga Thorvaldsdottir]

Some things to try/consider:

- If the problem has to do with Apple security, it sometimes helps to right click on the Mac App and select "Open", rather than double clicking on the app.

- If this is an M1 Mac, the Java included with the IGV app depends on Apple's Rosetta utility - so IGV won't run unless Rosetta is installed.

- If it's not even bringing up the IGV window, you might be able to see useful error messages if you launch it from the command line.

Download 'Command line IGV and igvtools for all platforms'; and then on the command line run igv.sh in the downloaded folder; let us know if it spits out any error messages. Note you'll need to have Java installed on your system (we test with Java 11 but we know that users have successfully run with some newer versions). 

Helga