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qiime2 / q2galaxy

Generate Galaxy tool descriptions automatically from QIIME 2 actions.
BSD 3-Clause "New" or "Revised" License
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No tools:unzip_collection, Flatten collection and Sort #52

Open Dong2843997826 opened 5 months ago

Dong2843997826 commented 5 months ago

Hi，@ebolyen I used docker to pull and run q2galaxy. When building my workflow, I found that there are no basic tools, such as unzip_collection, Flatten collection and Sort. How can I install these tools in q2galaxy?

Dong2843997826 commented 5 months ago

@Oddant1

Oddant1 commented 5 months ago

Hello @Dong2843997826.

What use case do you have for unzipping collections? You should be able to use individual elements of collections as inputs to other actions as necessary.

Additionally, QIIME 2 does not currently nest collections, so flattening isn't needed functionality.

Sorting is a potential nice to have in the future, but order also does not currently matter.

Dong2843997826 commented 5 months ago

@Oddant1.Thank you for your reply.Oh, I did add some other workflows.But I found that none of these tools, like unzip_collection, are available. If I want to use these, how should I add them?

Oddant1 commented 5 months ago

@Dong2843997826 are you saying the built-in galaxy tools for unzipping, flattening, and sorting collections aren't there? ex

If so, that would be an issue with your galaxy configuration itself that I'm not sure how to resolve. We don't have any tools that implement that functionality in QIIME 2.

Dong2843997826 commented 5 months ago

Well, @Oddant1，@ebolyen，I have these tools when I use docker-galaxy-stable, but q2galaxy doesn't. I wonder if q2galaxy doesn't install these tools by default.

ebolyen commented 4 months ago

That makes sense, I think one issue is there hasn't been an update of the galaxy docker image. Ideally we would set up our image a bit differently so the default tools would come along (and we wouldn't have to overwrite them as you see).

I think it makes sense to wait on this a bit, as the entire docker stack is in pretty bad shape for this and we should be able to fix it really easily at some point(tm).

@Dong2843997826, I would recommend using a public galaxy server instead of the docker image at this point. We need a more modern version of Galaxy to support QIIME 2 anyhow (the current image is a kind of hacked together proof of concept).