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Galaxy #40

Closed dsavchenko closed 5 months ago

dsavchenko commented 9 months ago
dsavchenko commented 8 months ago

Example of the automatic PR https://github.com/esg-epfl-apc/tools-astro/pull/46

What's missing now, is .shed.yml file generation. But here, need to decide where this info (at least description and long_description are needed) comes from. Does workflow creator need to create a file with some fields defined, or just provide full .shed.yml?

There is also uncertainty in how to bump tool version properly.

Otherwise, the basic tool creation works

volodymyrss commented 7 months ago

branches should be probably created right in org repo, not in your own. Else secrets are not used (and they should not be)

dsavchenko commented 7 months ago

branches should be probably created right in org repo

Yes, it is a configurable parameter

dsavchenko commented 6 months ago

I need your advice, @bgruening Is it possible to directly query the toolshed API to get the list of available versions of the specific tool (by tool ID) there? I only found tool version info in the galaxy instance API (for the installed tools, I guess), but in the toolshed API I only see revision hashes, and it's not clear how to match them with the tool version

bgruening commented 6 months ago

I don't know :-( can you explain your use-case? Maybe we can brainstorm how tomsolve it differently.

dsavchenko commented 6 months ago

I don't know :-( can you explain your use-case? Maybe we can brainstorm how tomsolve it differently.

This is for the bot to decide the version of the next autogenerated tool release. I thought of the toolshed to be a single source of truth for the latest version already available. But if this is complicated, I can rely on the version of the tool in the main branch of our repo https://github.com/esg-epfl-apc/tools-astro/ assuming it's the only one with CI configured to push into the toolshed

bgruening commented 6 months ago

I see. We use GitHub. We follow those recommendations for numbering https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html and then let our bot increase the number.

volodymyrss commented 5 months ago

@dsavchenko it seems ready and approved. Maybe let's merge it and make further changes with new PRs as needed? Or something essential is missing?

dsavchenko commented 5 months ago

@dsavchenko it seems ready and approved. Maybe let's merge it and make further changes with new PRs as needed? Or something essential is missing?

I wanted to merge it when the first generated tool is ready to be pushed to the toolshed (we are very close to this). I will re-request review

volodymyrss commented 5 months ago

@dsavchenko it seems ready and approved. Maybe let's merge it and make further changes with new PRs as needed? Or something essential is missing?

I wanted to merge it when the first generated tool is ready to be pushed to the toolshed (we are very close to this). I will re-request review

Ok, good, so I turn it draft.

dsavchenko commented 5 months ago

When https://github.com/oda-hub/nb2workflow/pull/102 is merged, the nb2workflow branch needs to be changed in Dockerfile_galaxy and this PR will also be ready. I will add CI/CD to build galaxy-related container separately in the future.

The first autogenerated tool PR https://github.com/esg-epfl-apc/tools-astro/pull/82 looks good now.