Description:

tibanna 5.4.3

Tibanna


Tibanna runs portable pipelines (in CWL/WDL/Snakemake/shell) on the AWS Cloud.

Install Tibanna.
pip install tibanna


Use CLI to set up the cloud component and run workflow.
# Deploy Unicorn to the Cloud (Unicorn = serverless scheduler/resource allocator).
tibanna deploy_unicorn --usergroup=mygroup

# Run CWL/WDL workflow on the Cloud.
tibanna run_workflow --input-json=myrun.json


Alternatively, use Python API.
from tibanna.core import API

# Deploy Unicorn to the Cloud.
API().deploy_unicorn(usergroup='mygroup')

# Run CWL/WDL workflow on the Cloud.
API().run_workflow(input_json='myrun.json')



Note: Starting 0.8.2, Tibanna supports local CWL/WDL files as well as shell commands and Snakemake workflows.
Note 2: As of Tibanna version 2.0.0, Python 3.7 (and lower) is no longer supported. Please switch to Python 3.11! Python 3.8 is also supported as a fallback, but please prefer 3.11 if you can.
Note 3: Starting 0.8.0, one no longer needs to git clone the Tibanna repo.

Please switch from invoke <command> to tibanna <command>!
We also renovated the Python API as an inheritable class to allow development around tibanna.

For more details, see Tibanna Documentation.

Also check out our paper in Bioinformatics.
A preprint can also be found on biorxiv.

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

Share

• Share on Facebook
• Share on Twitter