... install bioformats in Debian and Ubuntu

Bioformats is not packaged in Debian and therefore, not in Ubuntu either. To install it in a way that will make it play best with the rest of the system, following the expected standards, use the following (adjusting the download URL for the bioformats version you want):

 sudo mkdir /usr/local/share/java/  
 sudo wget http://downloads.openmicroscopy.org/bio-formats/5.1.3/artifacts/bioformats_package.jar \  
  -O /usr/local/share/java/bioformats_package-5.1.3.jar  
 sudo ln -s bioformats_package-5.1.3.jar /usr/local/share/java/bioformats_package.jar  

This mimics how java packages are installed by Debian.  The actual jar has the version on the filename, while the unversioned filename is a symbolic link to a specific version.  This allows you to have multiple versions installed while keeping one (usually the latest) as the default.

apt would install those files in /usr/share/java so we place them in /usr/local/share/java instead. Remember that the whole /usr hierarchy should be considered off-limits, only the package manager should change things there.  The exception is /usr/local.  You can think of /usr/local being the equivalent as /usr that is managed by the system administrator instead of the package manager.  From the Linux Filesystem Hierarchy Standard:

The /usr/local hierarchy is for use by the system administrator when installing software locally.
[...]
Locally installed software must be placed within /usr/local rather than /usr unless it is being installed to replace or upgrade software in /usr.