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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 updates for Cerebellin #146

Closed djcomlab closed 6 years ago

djcomlab commented 6 years ago

Finalization of ISA-related tools for the C release.

Still to do:

This PR should also address #139 #134. I expect this to be read to merge by end of today.

pcm32 commented 6 years ago

@djcomlab just added a commit to resolve conflicts arising from some parallel PRs that were merged on the phenomenal_tools2containers.yaml, but feel free to revert to previous commit and push --force if you already had a fix locally for the conflict. You seem to have a few tool containers that will require releasing, let me know if I can help with any of that.

pcm32 commented 6 years ago

I will resolve conflicts, since this are are job_conf stuff I fixed today!

djcomlab commented 6 years ago

Will have to postpone the fix for #141 until after the release. It's a problem upstream in ISA API that will need fixing.

djcomlab commented 6 years ago

Just to recap, this PR has some final fixes to the ISA create tool, updates all the ISA/mtbls slicer tools to consume the ISA-Tab datatype (there's now a choice in the tool UI to query directly MetaboLights studies or to use an isa-tab datatype history item), as well as adding a new tool "Get data files collection" that does the ISA slicing and produces a dataset collection if the data files are present in the incoming isa-tab data history item.

Some of the factor querying in the ISA slicer is a bit buggy, but this could be due to upstream bugs in ISA API or problems in the MetaboLights ISA-Tab metadata itself.

djcomlab commented 6 years ago

I think this is now as ready as it'll ever be!