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phnmnl / container-galaxy-k8s-runtime

PhenoMeNal runtime for Galaxy running inside a container orchestrator
Apache License 2.0
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Move to 18.01 #195

Closed pcm32 closed 6 years ago

pcm32 commented 6 years ago

This PR moves both our galaxy container and the setup for using the community images-based setup to Galaxy 18.01, plus our ISA (datatype) and Kubernetes runner changes (better handling of jobs on instance restart). This should be tested with helm charts galaxy version >= 0.4.0 and galaxy-stable version >= 1.5.5 probably.

I would appreciate if people could test this locally and try some tools before we merge.

This PR supersedes #191 to avoid mixing the ISA and Galaxy 18.01 changes and be able to apply them sequentially.

pcm32 commented 6 years ago

Further to @djcomlab's testing done on #191, if someone else could test this locally and see their tools working (given that 17.09 to 18.01 is a major version change), I would really appreciate!

Thanks!

ilveroluca commented 6 years ago

I'm working on it between talks at a conference. I've been making some changes to the "simplified" build script to build the containers. Once it's all up and running I'll test it on minikube.

sneumann commented 6 years ago

Hi, I have enabled the Jenkins build for this branch on http://phenomenal-h2020.eu/jenkins/job/container-galaxy-k8s-runtime/ which should help me testing these containers, as I don't have a local test environment.

pcm32 commented 6 years ago

These builds have release tags though, which will confuse the release spreadsheet. You would need to change somehow the Jenkins scripts to add a new different prefix. docker build and docker push should allow to test this locally without a Jenkins build.

pcm32 commented 6 years ago

Ok, containers are building and things work on a fresh minikube setup (0.25). I'm only bothered by https://github.com/bgruening/docker-galaxy-stable/issues/443 but I don't think it should further delay us. Will merge this now.

pcm32 commented 6 years ago

Apparently we need an additional review given changes, could you do the honours @sneumann? I have tested everything to work.