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Some documentation for planemo run#1102

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jmchilton merged 6 commits intogalaxyproject:masterfrom
simonbray:docs-planemo-run
Dec 15, 2020
Merged

Some documentation for planemo run#1102
jmchilton merged 6 commits intogalaxyproject:masterfrom
simonbray:docs-planemo-run

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@simonbray
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Particularly focussing on the new features in #1076.

It would be really appreciated if a few people who are informed about planemo could scan through the headings and suggest any other things I could/should include; quite likely there is some functionality I'm not aware of.

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Great tutorial @simonbray a few comments inline.

I think it would also be useful to show an example planemo conf at some point to demonstrate what happens if a profile or alias is created. The text file I mean.

unlike a new upload, doesn't result in any additional storage being used.

To run the workflow using a workflow ID, replace the workflow file path with
the workflow ID from the Galaxy server:
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I am kind of skating over how to get this - if galaxyproject/galaxy#10848 can be added I will write another sentence here.

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We could for the time being use the ID that is displayed when the workflow editor is open, do we?

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Not sure what you mean here? That it is displayed in the URL? I can't see it displayed on the page anywhere.

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https://usegalaxy.eu/workflow/editor?id=adb3676c3450a227 --> this is what I see when the workflow editor is open. And I assume this is the workflow-id.

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Yes, it is. I would prefer if the user could get it some better way than copying out of the URL, that's why I made the issue above. But yes, if this cannot be fixed in the near future, I'll mention this alternative here.

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I guess we can mention this here and go for it until we have a better way.

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_running_external.rst:248: WARNING: Literal block ends without a blank line; unexpected unindent.

That seems to be a legitimate warning.

@simonbray simonbray marked this pull request as ready for review December 11, 2020 12:00
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I think this is ready, though it would be great if #1101 were merged first.

@bgruening bgruening changed the title [WIP] Some documentation for planemo run Some documentation for planemo run Dec 11, 2020
@jmchilton
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Amazing - thanks so much!

@jmchilton jmchilton merged commit 38352b5 into galaxyproject:master Dec 15, 2020
@simonbray simonbray deleted the docs-planemo-run branch December 18, 2020 09:43
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5 participants