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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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ISA-Tab Viewer visualization plugin for ISA-Tab datatype #243

Closed djcomlab closed 6 years ago

djcomlab commented 6 years ago

This PR adds the ISA-Tab Viewer (the JavaScript one from https://github.com/ISA-tools/ISATab-Viewer) as a Galaxy visualization plugin to work with the ISA-Tab datatype.

This depends on https://github.com/phnmnl/galaxy/pull/35 but I'm sure we would all like this for the D-release!

pkrog commented 6 years ago

Hi @djcomlab , I've tried this branch in minikube, and uploaded MTBLS1 with raw data. However the ISA-tab display does not show me list of nmrML files. Is it intended?

djcomlab commented 6 years ago

If you look at the changes you can see that this PR only really adds the plugin to container-galaxy-k8s-runtime.

The current container-galaxy-k8s-runtime does not have a fully working implementation of the datatype preview, hence the PR I reference on the phnmnl/galaxy repo off this branch https://github.com/phnmnl/galaxy/tree/feature/release_18.01_plus_isa_enhancement. In my testing I have never seen any data files being displayed in Galaxy using container-galaxy-k8s-runtime.

The release branch of container-galaxy-k8s-runtime does not show up any data files because the Galaxy it uses relies on an out-dated isa-rwval. The phnmnl/galaxy used in the container needs to be updated and then made sure it is used in building container-galaxy-k8s-runtime.

djcomlab commented 6 years ago

The plugin doesn't actually render properly for some reason. I had it working fine on https://github.com/phnmnl/galaxy/tree/feature/isa_data_type_plus_enhancements but the rebase to https://github.com/phnmnl/galaxy/tree/release_18.01_plus_isa_runnerRestartJobs in this PR seems to break the plugin rendering.

djcomlab commented 6 years ago

Issues fixed, to work after https://github.com/phnmnl/galaxy/pull/35 is merged.

djcomlab commented 6 years ago

Closing in favour of phnmnl/container-galaxy-k8s-runtime#244 to base on latest release branch.