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igvtools not running, issue with java

I am having a hard time running igvtools from the command line on my Mac (MacOS Big Sur 11.2). I installed IGV 2.10.0 using the 'Command line IGV and igvtools for all platforms' link with the following code:

wget https://data.broadinstitute.org/igv/projects/downloads/2.10/IGV_2.10.0.zip
unzip IGV_2.10.0.zip

When I try running any program of igvtools (count for example, though I get the same error just trying to run help) I get the following error:

Using system JDK.
Unrecognized option: --module-path=IGV_2.10.0/lib
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.

If it should be useful, here are the results of 'java -version':

java version "1.8.0_281"
Java(TM) SE Runtime Environment (build 1.8.0_281-b09)
Java HotSpot(TM) 64-Bit Server VM (build 25.281-b09, mixed mode)

Any help on getting IGV and igvtools properly installed so I can run it from the command line? I could easily install the MacOS app and could run from there but I would really like to run from the command line.

Also, I had the same error when I tried an earlier version of IGV (2.9.5).

Thanks in advance.

igv jdk igvtools java
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written by williamtmills • williamtmills

2 answers

Command line version requires Java 11 (LINK) so you will need to install that.

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written by GenoMax GenoMax

Love simple fixes.. this worked perfectly, thanks so much!

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written by williamtmills • williamtmills

Alternatively you can create a conda environment and install this way, all the correct dependencies should install automatically.

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written by noodle noodle

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