Java runtime dependences and impacts

[jfouret]

Hi,

A lot of recipes defined here (macse, factqc for examples) needing only a java runtime environment depends on openjdk conda package that provides the whole java dev kit.

This dependencies is about 400 MB while a headless jre should be about 60 MB at most.

This can represent a unnecessary burden on storage space if multiple environment are provisioned on the same machine and it implies also avoidable data transfers.

In addition, when docker images are built in the biocontainers project the resulting container images are unnecessarily too big in size (cf BioContainers/containers#558).

Of note, there are no properly maintained jre package on conda, it seems. One solution would be to create a recipe for a java jre on bioconda and use it as a dependency in place of openjdk package after. There is a project providing a jre for multple architectures: https://adoptium.net/temurin/releases/.

Of note, I am not myself a regular user of bioconda direclty however I came onto this problematic while using biocontainer images.

Bests,