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The Galaxy project as Community partner #105
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Hi @B0r1sD ! Thank you for your request! We can proceed just like in #104. So here is the full checklist details:
Happy to help along the way and welcome onboard! |
Small update: collection/scripts/script_utils.py Lines 48 to 72 in 5327dac
This simplifies the compatibility script needed from a partner, e.g. ilastik example, so now almost only an analog to collection/scripts/check_compatibility_ilastik.py Lines 16 to 25 in 5327dac
is needed to implement the compatibility check. Hope this makes things easier now and more maintainable in the future! |
Hey there Bioimage zookeepers!
We would like to explore the possibility into making the Galaxy project an official community partner at the BioImage Model Zoo. This proposal originates from the Image Analysis Community that makes use of your service, with the Galaxy tool wrapper Process image using a BioImage.IO model which uses Galaxy's computational resources to analyze images with models from your database.
We would like to strengthen this connection, so it's easier for Galaxy users to fetch data from BMZ, and preferably also easier for users to contribute models/data back to you.
Galaxy is a free, open-source system for analyzing data, authoring workflows, training and education, publishing tools, managing infrastructure, and more.
The Galaxy users interested in this tool could contribute their model/image creations after this connection has been implemented. On our side, we would create a tool that gets data from BMZ and redirects the user back to history with the data in their history, ready to run analyses.
Examples where such connection already exists are
UCSC Main tool
,EBI SRA
,... which you can find in the tools tab of https://usegalaxy.eu, https://imaging.usegalaxy.eu/,... as tools are maintained in a seperate repository such as https://github.com/galaxyproject/tools-iuc.Main Galaxy codebase: https://github.com/galaxyproject/galaxy
However the imaging subdomain is part of the European Galaxy instance, not the .org one.
Galaxy has an active community with a bunch of contributors. @wm75 is the expert on these data source implementations and can help with the technical details. The Image Analysis Community will be on top of this connection and internally distribute maintenance.
If this request makes sense to your team, we can discuss further how this could be implemented technically on both sides. Let us know if you need more information, and I'll be happy to provide it. Thanks for the consideration!
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