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ABOUT.rst

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BioBlend is a Python library for interacting with the Galaxy API.

BioBlend is supported and tested on:

  • Python 3.8 - 3.12
  • Galaxy release 19.05 and later.

BioBlend's goal is to make it easier to script and automate the running of Galaxy analyses and administering of a Galaxy server. In practice, it makes it possible to do things like this:

  • Interact with Galaxy via a straightforward API:

    from bioblend.galaxy import GalaxyInstance
gi = GalaxyInstance('<Galaxy IP>', key='your API key')
libs = gi.libraries.get_libraries()
gi.workflows.show_workflow('workflow ID')
wf_invocation = gi.workflows.invoke_workflow('workflow ID', inputs)

  • Interact with Galaxy via an object-oriented API:

    from bioblend.galaxy.objects import GalaxyInstance
gi = GalaxyInstance("URL", "API_KEY")
wf = gi.workflows.list()[0]
hist = gi.histories.list()[0]
inputs = hist.get_datasets()[:2]
input_map = dict(zip(wf.input_labels, inputs))
params = {"Paste1": {"delimiter": "U"}}
wf_invocation = wf.invoke(input_map, params=params)

About the library name

The library was originally called just Blend but we renamed it to reflect more of its domain and a make it bit more unique so it can be easier to find. The name was intended to be short and easily pronounceable. In its original implementation, the goal was to provide a lot more support for CloudMan and other integration capabilities, allowing them to be blended together via code. BioBlend fitted the bill.