Skip to content

BioinformaticsArchive/bioblend

 
 

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

BioBlend is a Python (2.6 or higher) library for interacting with CloudMan and Galaxy's API.

Conceptually, it makes it possible to script and automate the process of cloud infrastructure provisioning and scaling via CloudMan, and running of analyses via Galaxy. In reality, it makes it possible to do things like this:

  • 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)
  • 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)

Note

Although this library allows you to blend these two services into a cohesive unit, the library itself can be used with any single 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

A python library for interacting with CloudMan and Galaxy API

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published