Permission error opening IGV_2.9.4 on new MacBook Pro

[Pedro Forde]

Hi,

I am running macOS Big Sur (version 11.3) on a new MacBook Pro with an M1 chip.  I can download IGV_2.9.4 with no problem.  However, when I try to start IGV, I get the following error message:

     You do not have permission to open the application "IGV_2.9.4".

     Contact your computer or network administrator for assistance.

This is a personal computer, so there is no administrator (other than me).  I spent about three hours on the phone with Apple support, but they are stumped.  I've used IGV on a desktop Mac many times over the past year and have never had any problem getting it to work.  Any suggestions?

Thanks for your help.

Carl

[Helga Thorvaldsdottir]

Hi Carl,

Unfortunately we don't have access to an M1 Mac to try to reproduce this ourselves, but lets see if we can figure this out!

A few questions:

Exactly which version of IGV 2.9.4 are you downloading? For example is it the MacOS app with Java included from the IGV downloads page?

Which folder do you download it to? 

How do you launch it?

Helga

[Pedro Forde]

Hi Helga,

I tried both MacOS versions (with and without Java).  I downloaded them to my downloads folder and attempted to launch IGV from there.

When this didn't work, I moved IGV from the downloads folder to the applications folder and tried to launch IGV from there.  None of these options worked.

I always get the same error message.

Carl

[Pedro Forde]

I downloaded these versions of IGV from the IGV downloads page.

[Helga Thorvaldsdottir]

There are a few things I can think of:

1) Right-click on the app file and select open. That sometimes works to bypass issues with permissions. Although I assume the Apple support folks already suggested that.

2) The first time you run IGV after downloading it via a browser, the Mac pops up a dialog saying that this is a file downloaded from the internet, and asks if you are sure you want to open it. Did you see that and give approval? If not,  I do notice that the message includes which web browser I used. Are you using one of the common web browsers to download the app?  If not, maybe try another one to do the download (for example, we commonly test using Safari, Chrome, Firefox).

3) If you don't remember seeing that message - perhaps try loading a different version of IGV to start fresh and see if the message appears. Downloading old versions can be done via the Archived Versions link on the Download page; here's a direct link to where you can find all the 2.9.x versions. Try running the older version of IGV and see if it now asks for permission.  If not, is that something the Apple support people discussed with you? I have no idea why it wouldn't show. But, if it does now ask for permissions,  does IGV still not open?

4) Alternatively, you can run a command-line version of IGV that is not an Apple App. This will require Java to be installed on your system. We test with Java 11, but I know of users who have successfully run IGV with later versions of Java. Download the zipped up folder of the command line version from the Downloads page (or here's a direct link to the IGV 2.9.4 command line version). Then in a Terminal window go to the downloaded folder and run ./igv.sh

5) Finally, since the error you've been seeing comes from the OS even before IGV is launched, I don't think anything in your IGV preferences is affecting this. But to remove all old IGV preferences, you can remove or rename the igv folder that's in your home folder.

Let me know how it goes.

Helga

[Pedro Forde]

Helga,

Thanks for the suggestions.  I will try them.  IGV has been a wonderful research tool, so I am hoping to get it running.

Carl

[Pedro Forde]

Helga,

I was finally able to run IGV_2.9.4 by installing Rosetta, a utility that allows an M1 Mac to run software written for an Intel-based Mac.  

I stumbled upon this solution through roundabout means.  When I tried your suggestion to run IGV from the command line in terminal mode, 

Big Sur responded by saying that I needed to install Java.  I went to the Java website and started to download Java 8 which generated 

a prompt to install Rosetta.  I installed Rosetta and then on a hunch went back to the IGV download site and downloaded IGV 2.9.4 with Java.

Double clicking on IGV 2.9.4 started IGV with no further problems.  IGV's behavior appears normal.

The Apple support person said that Big Sur should have prompted me to install Rosetta yesterday when I first tried to run IGV 2.9.4.   He

didn't know why this didn't happen.  In any event, IGV is now running on my MacBook Pro, and I am a happy man.

 At some point in the future, IGV will apparently need to be recompiled to run on Apple's M1 machines.  Apple is moving it's "ecosystem" from 

the Intel chips to its own M1 chips.

Thanks again for your help!

Best,

Carl 

[Helga Thorvaldsdottir]

Thank you for the detailed update. I'm glad that you finally got things working!