IGV_2.7.0 won't run on Mac OS Catalina

[BenWittner]

Hi, I recently made the mistake of upgrading my Mac to the Catalina OS. After I did that, the version of IGV that I had was not repainting the screen properly. So I deleted it and downloaded IGV_2.7.0. When I double click on that I get the attached error message. I don't know how to convince the Mac to run it anyway. Any help would be appreciated. Thanks. -Ben

[jrobinso]

Thanks for the report, unfortunately we don't have Catalina and were unaware of this.    I can't give an ETA on Catalina support right now.

As a workaround you could try running  a command line version.  We don't have one for the Mac on the Downloads page, but do on the night snapshot page.   Here's a direct link:  http://data.broadinstitute.org/igv/projects/downloads/snapshot/IGV_Mac_snapshot.zip.     After unzipping you will need to use a terminal,  cd to the "IGV_Mac_snapshot" directory and execute

./igv.command

Could you please let us know if this works or not.

[jrobinso]

Here's another suggestion, from a web search. Try right-clicking the IGV app and selecting "Open" from the popup, rather than double-clicking.

https://www.fireebok.com/resource/how-to-fix-that-app-can-not-open-on-macos-catalina.html

[BenWittner]

That worked. It still popped up the message saying it could not run it, but there was an “open” button added. When I clicked that button it ran. Now, double-clicking runs it as does single clicking on its icon in the dock. So I guess I can’t test your command line suggestion, but I’m happy. Thanks very much. I guess I should have web searched for work-arounds to the general problem, as you did.

From: Jim Robinson notifications@github.com Reply-To: igvteam/igv reply@reply.github.com Date: Tuesday, October 15, 2019 at 3:14 PM To: igvteam/igv igv@noreply.github.com Cc: "Wittner, Ben, Ph.D." Wittner.Ben@mgh.harvard.edu, Author author@noreply.github.com Subject: Re: [igvteam/igv] IGV_2.7.0 won't run on Mac OS Catalina (#713)

    External Email - Use Caution

Here's another suggestion, from a web search. Try right-clicking the IGV app and selecting "Open" from the popup, rather than double-clicking.

https://www.fireebok.com/resource/how-to-fix-that-app-can-not-open-on-macos-catalina.html

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/igvteam/igv/issues/713?email_source=notifications&email_token=AJL44R355O5DIQYR2RYXQDDQOYJAHA5CNFSM4JBAVAF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBJ4ZIY#issuecomment-542362787, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AJL44R77YJKXSBJMZDRGP6LQOYJAHANCNFSM4JBAVAFQ.

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

[brainstorm]

@jrobinso How's the notarization process going? I've had a few questions about it recently from new users installing it on Catalina :-S

[davideby]

@brainstorm Yeah, we're starting to see an uptick on that front as well.

There are issues with the JDK included in our Mac.app. Technically we can notarize it with warnings, but we're about to cross an Apple-imposed deadline where those warnings will now be considered errors.

We're in a bit of a holding pattern to see how the JDK developers will deal with it. There are some things we might be able to do on our own (looking at alternate JDKs, for example), but as usual it's a matter of competing priorities.

The workaround on our Downloads page seems to be working OK for most users, though it's not ideal.

[brainstorm]

Any news on this front? New users keep bumping into this :-S

[davideby]

Hi @brainstorm,

Good timing.

@jrobinso just released 2.8.3, which I've signed and notarized and posted for download. This is our first macOS notarized release and should in theory fix this issue, plus the issue of accessing reserved file locations. This should be possible without needing to grant special access, etc. I don't actually have Catalina, though, so none of that has been tested yet.

Let us know if you hit anything further along those lines.

Thanks, David