Problem running IGB on linux
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6.3 years ago
kirannbishwa01 ★ 1.4k

I am trying to run IGB in my linux ubuntu. The previous version were able to run using java but recently the one run using "sh" are not running.

I tried: sh IGB_unix_8_5_2.sh

and also sudo sh IGB_unix_8_5_2.sh

But, no luck. I am getting the following message:

rm: cannot remove '/home/everestial007/.install4j': No such file or directory
Unpacking JRE ...
Preparing JRE ...
IGB_unix_8_5_2.sh: 197: IGB_unix_8_5_2.sh: bin/unpack200: Permission denied
Error unpacking jar files. The architecture or bitness (32/64)
of the bundled JVM might not match your machine.

Integrated-genome-browser shell IGB java • 2.4k views
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Have you checked if "The architecture or bitness (32/64)of the bundled JVM might not match your machine"
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I checked that one and searched for solutions on google. Tried several things, but no luck !

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6.3 years ago
dcnorris ▴ 270

Hi kirannbishwa01,

The trouble with running the binary (i.e. the .sh installer) is the binary is built for 64 bit machines. The zip file is the suggested workaround, but unfortunately requires you to manage your own java runtime version. Please make sure you only use the very latest java version (e.g. Java SE Runtime Environment 8u73) to run IGB since there have been several bugs affecting our software in recent releases of the Java runtime. Some of those bugs are likely causing the performance problem you are seeing. Please let me know if the problem persists after ensuring you are on the latest java runtime version.

Best Regards,

David Norris

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Thanks dcnorris !

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6.3 years ago
h.mon 34k

At the IGB SourceForge page you can find a zip file with a compiled "portable" IGB. Just unpack and run the run_igb.sh script.

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I am not finding any files with that specific name. I already tried running IGB_unix_current and IGB_unix_8_5_2.

Can you provide me a link to the specific file you are mentioning.

Thanks,

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Thanks, that worked.

But, I am having another problem After loading the IGB is taking up all the computer cores and computing power (the CPU usage bumps immediately to above 89%) and after about 5 mins the computer just freezer. The only way out is to kill the process. I have already tried it dozen times but its still the same.

There should be a way to work this problem out - let me know if  you know it.

But, thanks a lot !