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Upgrade outputs ODV #171

Closed Marie59 closed 1 year ago

Marie59 commented 1 year ago

I added a few lines in the wrapper in the hope to be able to get ODV's outputs in the galaxy history (https://github.com/usegalaxy-eu/galaxy/issues/170). Indeed, for now I can't use ODV outputs and use them as inputs in other tools. Are the changes that I made relevant @bgruening ? Sorry if I am totally lost here.

bgruening commented 1 year ago

Do you know why you need to be in the output directory when starting the application?

Marie59 commented 1 year ago

Do you know why you need to be in the output directory when starting the application?

No need. That's not what I was aiming at doing it's an useless line that I wrongly copy paste from my test I think. From what I understood (which might be not that much) the outputs folder in the ODV app is not link to the Galaxy history outputs. Is the cp command enough to do so ?

Marie59 commented 1 year ago

Oh okay that's how I can do it ! Thanks !!

bgruening commented 1 year ago

@Marie59 can you check if this is working now?

Marie59 commented 1 year ago

It's not working I have this error ln: target './output/' is not a directory: No such file or directory. Could it be because now there is'nt this lin in the xml mkdir output && ?