Hi Pierre,

After some searching I found the answer on a blog (can't link it here) - I thought the shell script was called automatically, that was my mistake there.

The missing steps were:

1. Extract all the .jar files to ~/mipav/plugins before installing,
2. Edit the bash script run-cbstools-mac that is within ~/mipav/plugins/ to reflect the correct path.
3. run run-cbstools-mac as a shell script (have to chmod +x run-cbstools-mac it as well)

Optional:
in your .bash_profile you can alias the cbs command via the following:
alias cbstools='source ~/mipav/plugins/run-cbstools-mac'

Cheers!