IGV app won't open

[Seth Pincus]

I have a Macintosh Powerbook running OS Monterey 12.5.1. I downloaded the MacOS IGV app (both with JAVA built in or requiring external JAVA).

Each time I try to open the app, it briefly opens, but then shuts down. Fearing my University's security software was interfering, I asked IT and received the following reply: "MSU does block Oracle Java installs, so that could be something to consider. We recommend to install Amazon Coretta (Java developed by Amazon which is updated and free)". Will this work? Do you have other recommendations?

Not sure if I have an IVG0.log file.

Thank you

[igv-help]

Our "with Java" bundle uses OpenJDK, which is the same Java as Amazon Coretto. However since that's not working for you I suggest you follow your IT departments advice.  

First make sure you don't have a Java installed already,  you can do this from a command prompt by typing "java --version".     Then install Amazon Coretto 11 and use the "requires external Java" bundle.   I'm not hopeful that this will work but it will allow you to take the next step with your IT department.

Jim

[Dan Kolis]

Hi,

I run it with this script on Ubuntu:

echo Run igv from any directory
cd ~
cd 'About_WIXM/Venter V3 simulation/Python_and_Dan/IGV'
cd IGV_Linux_2.14.1
prefix=.
java -showversion --module-path="${prefix}/lib" -Xmx8g \
        @"${prefix}/igv.args" \
        -Dapple.laf.useScreenMenuBar=true \
        -Djava.net.preferIPv4Stack=true \
        --module=org.igv/org.broad.igv.ui.Main "$@"
echo Started running or something good I hope

A few other files are attached. 

Look at each attachment, probably kind of carefully..

Good luck, the tragedy of Apple suffola is a heavy burden.
Regards,

Daniel B. Kolis

my ref: igv, broad, harvard, 13 Sep 2022, nafl, https://groups.google.com/g/igv-help/c/SXsCfuoFniA

[James Robinson]

I'm sorry, what is this in reference too, and do you have a question for us? 

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[Dan Kolis]

I just saw 'won't open, Apple' and noticed the corresp named a log file I saw fly by. I visualised the idea of an offbeat circumstance ( non mainstream java, - yuck ).

Sometimes a teeny hint from a similar install that worked, is pretty helpful.

I had no troubles worth mentioning really. I had just finished the DIY 'how this is built' I always do for myself. Pretty often the same item tilts the cart to: "WOW ! It's running !" ... and somebody else gets a happy moment from seeing some detail in my stuff.

No problem ...

Thanks,
Daniel B. Kolis 


my ref: igv, broad, harvard, 13 Sep 2022, nafl, https://groups.google.com/g/igv-help/c/SXsCfuoFniA, second today back 14:40 e

[igv-help]

OK, thanks for the tip.

[Dan Kolis]

ff my stand alone situation adds value; spec some experiment / procedure and I will do it if it's useful.

I could .tar or .zip up a sizable heap of history of CLI I pecked in too,,,,

I didn't follow the directions almost at all... but had it running in 20 minutes 'all the way' and know where the files land etc. So, well, thats good enough for an old guy like me. Running under Ubuntu. Ran it with e Coli, can bee base pairs, etc. Started make 7 times over 2 days. It's running without specific badness at all it appears.

my ref: igv, broad, harvard, 13 Sep 2022, nafl, https://groups.google.com/g/igv-help/c/SXsCfuoFniA, 18:51 est

[James Robinson]

The problem you reference in your post is an internal security issue at a specific institution, it is not an issue of knowing how to start IGV.   i would hope if you follow our directions it would not take 20 minutes to figure out how to start IGV, it ideally will take no time.

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[Seth Pincus]

Re post "IGV app won't open". I have downloaded Amazon Coretta, and it runs the app just fine. Thanks all for the suggestions. 

Seth Pincus

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[Dan Kolis]

Great that works. I know Google Cloud firebase etc well but nothing about AWS.

So much to learn in this crossover stuff between cloud and heap-of-your-own-computers, etc. 

How exotic to have a custom compiler ? well package or whatever.
" Amazon Corretto is a no-cost, multiplatform, production-ready distribution of the Open Java Development Kit (OpenJDK). Corretto comes with long-term support that includes performance enhancements and security fixes. Corretto is certified as compatible with the Java SE standard and is used internally at Amazon for many production services. With Corretto, you can develop and run Java applications on operating systems such as Amazon Linux 2, Windows, and macOS."

Probably the comfort level for mac uses hops up with this thing existing, specifically...

Google cloud leans into node as-is massively, but there are lots of permissions for different ways to have exe's hop in and out of that cloud too; None as orderly as this, I suspect.

Regards to all,

Daniel B. Kolis

my ref: igv, broad, harvard, 14 Sep 2022, nafl, https://groups.google.com/g/igv-help/c/SXsCfuoFniA, 14:08 est, SPincus, JRobinson