Docker/Java advice for utils?

[Jaclyn Andricovich]

Hello, 

I have been running the HiC-Pro pipeline in Docker with great success. Thank you Nicolas Servant!

Background

I now have allValidPairs files that I would like to convert to .hic files for downstream visualization/analyses, ideally using the "hicpro2juicebox.sh" util inside the container. [*I don't have Ubuntu on this PC, currently running HiC-Pro_3.0.0 in Windows 11]. 

The hicpro2juicebox.sh script starts to run, but eventually exits due to Java error [in line 152], I assume because Java is not in the container.

Question
Can anyone advise how to edit the Dockerfile to include Java?(https://github.com/nservant/HiC-Pro/blob/master/Dockerfile)

Thanks in advance for any help or tips you can provide!

Sincerely,

Jaclyn Andricovich