carandraug

Install Bioformats in Debian and Ubuntu

bioformats sysadmin

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.