Hello.
Does anybody know if this tool works in Galaxy?
Thank you.
Welcome, @Alexandra
Did you see the help on the tool form? Publication? The link out to the graphics at the others site? The tool is a sort of “pipeline” that bundles other tools and makes then run all together.
That means most (everything?) it is doing can be done with other tools directly, and you’ll find many of those also in Galaxy. You can string those “other” tools into a workflow, which gives you much more control and visibility into what is actually being done at each step.
If so, the version in Galaxy is just one part of the entire original pipeline. It is the part where some other assembly result is then submitted to this tool to break it down in other ways using different tools. It seems to be for exploratory reasons, to answer questions like: were your original assembly/binning parameters a good fit? Could they be improved? How?
I haven’t used it before but started up a test run using the very small test data associated with the tool. The base inputs include two parts:
- a final assembly sequence (fasta output from another tool)
- and, the reads involved in that assembly (fastq, maybe filtered by mapping back to that assembly).
Which tool to originally assembly with is left vague on purpose, for flexibility, or that is how I interpreted it, but see the publication for real data and tool examples. These are just my guesses from ~5 minutes of a very quick scan!
https://usegalaxy.org.au/u/jennaj/h/imported-from-archive-test-metawrap
- UseGalaxy.eu == failed (technical reason)
- UseGalaxy.org.au == still executing, curious about what happens
- UseGalaxy.org == not hosted at all
What I am more sure about: I don’t think this tool is being actively supported in Galaxy (but someone can correct me!). Why? I did see that the original author of the tool (the baseline pipeline) states at Github that they have moved on to other projects, so them not supporting at the source is a pretty good reason to not support it other places. Over time, unsupported software can become fragile as technology evolves. Sometimes that burden is not worth it.
We can follow up depending on your interest and needs, and how the AU server is working with the test above.
And, for the alternatives, I would suggest starting here, and you can explore plus ask more questions. 
Update!
It seems I needed to just be a bit more patient! The output files were written out at the UseGalaxy.org.au server. They look Ok to me, so please also try the tool there to see if it works for you!
I’ve also submitted administration issue to the UseGalaxy.eu team about the technical item with the tool execution. Maybe they can solve it. 
The details are here if you would like to follow along, or add in any more comments. Configuration issue with metawrapmg_binning · Issue #1297 · usegalaxy-eu/infrastructure-playbook · GitHub
Well, the AU job finished, and didn’t fail, and claims to have written out the outputs but didn’t actually add in any data to the output collection folders.
Let us know if you want follow up. And, if you have real data, and want to share your history, we can use that to reach out to the AU administrators to see what is going on.
Hope this helped!
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Hello,
Yes, thank you, I will try it and come back to you.
Best regards,
Alexandra
Great, thanks @bjoern.gruening !
And, @Alexandra the simple test worked fine for me at the EU server. The test history is here as a reference → https://usegalaxy.eu/u/jenj/h/test-metawrap
Thank you very much! I will try it !
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