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.