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galaxyecology / tools-ecology

Galaxy Tools maintained and developed by the GalaxyE community
MIT License
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Argo decoder tool #105

Open Marie59 opened 5 months ago

Marie59 commented 5 months ago

So, this is a batch tool using a docker image as a requirement. To work properly we will need to add a line there : https://github.com/usegalaxy-eu/infrastructure-playbook/blob/master/files/galaxy/tpv/interactive_tools.yml#L52 to change the user.

The docker image is heavy so we'll see if it's possible to use it. The image once build is publicly accessible there ghcr.io/euroargodev/coriolis-data-processing-chain-for-argo-floats:061a-galaxy For now the docker file is on a private gitlab but will soon be on a public github thanks to @leobr29.

I am starting this PR to see what needs to be improve and see the best ways to make this new tool work. This is a 1st version to make a demo for the Argo community in April. The aim is then to improve the tool (for instance remove all the zip and make more readable inputs and outputs) and create a workflow where we can access the argo data, decode them, and then visualize and analyze them with scoop-argo, ODV and DIVAnd.

I am not sure I'm making the PR in the right place. I put it with the other argo related tool. Thoughts ?? Comments ??

Plus, I don't know how to make planemo test work (or if it's even possible) with a docker as a dependence

Marie59 commented 5 months ago

@bgruening Is the tool good enough for a 1st try to deploy it or not ?

bgruening commented 2 months ago

.shed.yml is missing I think