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ABOUT.rst

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BioBlend is a Python library for interacting with Galaxy and CloudMan APIs.

BioBlend is supported and tested on:

  • Python 3.6, 3.7, 3.8 and 3.9
  • Galaxy release_17.09 and later.

BioBlend's goal is to make it easier to script and automate the running of Galaxy analyses, administering of a Galaxy server, and cloud infrastructure provisioning and scaling via CloudMan. 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')
gi.workflows.run_workflow('workflow ID', input_dataset_map)

  • 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.run(input_map, "wf_output", params=params)

  • Create a CloudMan compute cluster, via an API and directly from your local machine:

    from bioblend.cloudman import CloudManConfig
from bioblend.cloudman import CloudManInstance
cfg = CloudManConfig('<your cloud access key>', '<your cloud secret key>', 'My CloudMan',  'ami-<ID>', 'm1.small', '<password>')
cmi = CloudManInstance.launch_instance(cfg)
cmi.get_status()

  • Reconnect to an existing CloudMan instance and manipulate it:

    from bioblend.cloudman import CloudManInstance
cmi = CloudManInstance("<instance IP>", "<password>")
cmi.add_nodes(3)
cluster_status = cmi.get_status()
cmi.remove_nodes(2)

Note

Although this library allows you to blend these two services into a cohesive unit, the library itself can be used with either service irrespective of the other. For example, you can use it to just manipulate CloudMan clusters or to script the interactions with an instance of Galaxy running on your laptop.

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 fit the bill.