README.md

Tibanna

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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')

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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.