Confused about juicebox and juicertools jar releases

[vidal-adrien]

Dear Aiden lab

I am trying to get the most recent version of juicebox and juicertools for linux, i.e. the most recent jars.

Looking at the [https://github.com/aidenlab/Juicebox/wiki/Download](download wiki page) of this repository, reached from your https://www.aidenlab.org/software.html, there are only links to a jar file up to 1.11.8.

For 2.XX.XX, the "Github Releases" link sends to the releases of this repository but they are jar files for juicertools, not juicebox. The latest version here is 2.20.00 from oct 2022.

Looking at the readme of this repository, I find the message about the split between the different modules with links to repositories sending to the various repositories each with a 3.X.X version dated Dec 2021.

I would think that all these 3.X.X versions should be the most up to date but this repository has more recent commits, a more recent release of juicertools and is still the one linked from your website.

Which jars of juicebox and juicertools should I get ?
Is the 3.1.4 juicebox jar from the juiceboxGUI reposiitory more recent than the 2.17.0 windows and apple installers of juicebox ? Most of my colleagues will likely prefer using these versions than a jar on their windows/apple systems so I'd like to be sure we have comparable versions.

Thanks in advance,
Adrien Vidal

[sa501428]

Hey @vidal-adrien !
Apologies - we will get this README cleaned up asap. The latest Juicebox release is under Github Releases under the tag for v2.16.0.

[vidal-adrien]

Thank you. So if I understand correctly:

• This repository is where we get all the "juice*" software.
• Each release only has the jars of the programs that have been updated.
• The latest juicertools jar is 2.20.0.
• The latest juicebox jar is 2.16.0.
• The split repositories are irrelevant.

All correct ?