Hello,
I’m trying to use the galaxy api & I’m currently reading through the docs ( Quickstart — Galaxy Project 21.01 documentation )
but from the start I’m experiencing problems
It asks me to use a file called " display.py " but I cannot find it anywhere in my galaxy files.
I’m not sure whether this is an issue with the docs or whether I have downloaded something incorrectly.
Could someone enlighten me?
Thank you in advance!
ps. I am a beginner when it comes to working with APIs
Hi @stvlar,
you can find that file in /galaxy/scripts/api/. Do not hesitate to ask any questions you may have.
Regards
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Thank you so much I found it!
I have managed to connect to the API and run some tools and workflows but I’m having trouble getting the results via API call to my local computer. I’m using BioBlend and it doesn’t mention result retrieval in the docs API documentation for interacting with Galaxy — BioBlend 0.15.0 documentation
Do you have any insight on this?
Thank you in advance!
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I’m asking specifically because I want to make the results downloadable for people other than me
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Hi @stvlar,
I asked one of the people in charge of BioBlend; I’ll provide you a response in the next hours.
Regards
Hi @stvlar,
when you run a tool through Galaxy / BioBlend, it will produce some datasets as outputs. If you know the dataset id, you can then download it using the gi.datasets.download_dataset() method. To make them available to other users, you can use the publish_dataset() method.
Hope this helps?
Simon
3 Likes
Thank you so much!
Thank you both so much for your help!
Is there anyway for gi.datasets.download_dataset() to work after getting results? Because when I use it now it doesn’t return anything since the process hasn’t been completed yet
Thank you again!
Do you mean that the Galaxy job which creates the dataset hasn’t completed yet (it is still orange in the UI?) In that case, yes, the method will wait until the dataset reaches the ok state.
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Yes basically I want to write a script that will upload data, will wait for the process to complete and then download the results but it’s not waiting for the process to complete so I’m never getting the results.