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Scripting Galaxy using the API and BioBlend

Contributors

AvatarOlivia Doppelt-Azeroual AvatarFabien Mareuil AvatarNicola Soranzo AvatarDannon Baker

Questions

Requirements

last_modification Last modification: May 27, 2021

Galaxy API

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Interacting with Galaxy: UI vs. API

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Galaxy API functionalities

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RESTful API

.left[REpresentational State Transfer (REST) is the architectural style of the World Wide Web:]

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API requests

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API requests

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JSON format

.left[JavaScript Object Notation https://www.json.org/] JSON logo

{"history_id": "b5731bb49a17bf50",
 "id": "df06cc665d85b6ea",
 "inputs": {"0": {"id": "bbd44e69cb8906b51528b5d606d1fdd0",
                  "src": "hda"}},
 "model_class": "WorkflowInvocation",
 "outputs": ["bbd44e69cb8906b528819eaaff340ecd",
             "0ff30b4e2a4bed9e"],
 "state": "scheduled",
 "update_time": "2015-07-03T19:28:39.544574",
 "workflow_id": "56482e194d798eb6"}

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Status codes and errors

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How to access a REST API

.left[With anything that can communicate over HTTP:]

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Security

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Advanced Galaxy API config

.left[Options in config/galaxy.yml:]

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Galaxy API Modernization

.left[Moving to FastAPI]

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Galaxy API pros and cons

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BioBlend

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BioBlend features

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Tutorials - part 1

We have prepared some tutorials as Jupyter notebooks, which can be executed online with Binder at https://mybinder.org/v2/gh/nsoranzo/bioblend-tutorial/main

Walk-throughs:

Exercises:

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BioBlend limitations

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BioBlend.objects

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Tutorials - part 2

More Jupyter notebooks which can be executed online with Binder at https://mybinder.org/v2/gh/nsoranzo/bioblend-tutorial/main

Walk-throughs:

Exercises:

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References

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Key Points

Thank you!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors! Galaxy Training Network This material is licensed under the Creative Commons Attribution 4.0 International License.