caMicroscope Dockerfile structure

Image-decoders is the base Dockerfile for caMicroscope SlideLoader that serves metadata and iipsrv that serves images. It installs OpenSlide and BioFormats. OpenSlide is installed to its normal location and BioFormats is installed to /usr/lib/java. BFBridge the BioFormats wrapper is installed to /root/src (/root/src/BFBridge/c/bfbridge_basiclib.c, etc.) as /root/src is the project root for projects deriving from this source Dockerfile.

The Dockerfile also sets BFBRIDGE_CACHEDIR to /tmp/ and BFBRIDGE_CLASSPATH to /usr/lib/java. BFBRIDGE_CLASSPATH is expected to be a path to a single folder containing required Jars (unlike CLASSPATH, which is the standard Java classpath env variable allowing multiple paths and jars). BFBRIDGE_CLASSPATH is more stringent than CLASSPATH since the C wrapper scans it manually and it cannot parse the Java CLASSPATH format.