Add OpenJDK:8 as a docker dependency

Right after onboarding into dockstore while deploying CGP Sanger pipeline, I’ve been greeted by this:

Dockstore requires Java version 1.8 and above.

On (legacy) HPC clusters this is bound to be a problem… would you accept a pullrequest that pulls jre 8 as a default runtime instead of relying on the host’s (deprecated) preinstalled JAVA?

[denis-yuen]

@brainstorm Hi, I think there are two parts to this answer

1. Sounds good, an option to point at a version of Java not on the PATH makes sense to me.
2. I have to add a caveat that we test with Oracle JDK 8. OpenJDK 8 will probably work (knock on wood), but it simply is not something we have tested with yet.

[denis-yuen]

Hi, No, ironically, we haven’t actually run the dockstore command-line itself inside a Docker container.

Rather, the normal flow of things is on a particular host, Docker and Java 8 are installed, then cwltool. When you run the dockstore command-line, it does a bit of file provisioning, then calls cwltool, which starts a Docker container (CGP-Somatic-Docker) in your case, and then finishes up when the container stops. (We’ve run through Somatic Docker many times in this fashion)

These two pages of the tutorial describe this: https://dockstore.org/docs/getting-started-with-docker https://dockstore.org/docs/getting-started-with-cwl

Note that the dockstore command-line runs on the host and that’s where (Oracle) Java 1.8 is important. That’s why I thought you were either trying to a) try out the dockstore command-line with OpenJDK installed on the host when running on hosts that cannot install 1.8 or b) run the dockstore command-line in a docker container to work around this.