Picard issues with the pipeline

Debian-med team has packaged the new version of picard-tools, which is not compatible with our pipeline when installing "normally". Our pipeline needs all individual .jar files, which are not installed in the normal way (a single picard-tools wrapper script is installed). As debian-med version is higher than ours, and we're using their repository to download other dependencies, apt is getting their picard-tools version. 

I've pointed to our specific version of picard-tools by the moment, but maybe we can take a look at this fact.

As @chapmanb is making a few changes in the pipeline now, maybe he can advise us with this matter? 

Thank you very much!