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.

Note2: Python2.7 support is deprecated now (0.7.0 or after)! Please switch to Python3.6!

Note3: 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.

Note4: Tibanna_4dn (extension of Tibanna) is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna_4dn has moved to its own Github repo since version 0.10.0.

Nore5: For more details, see Tibanna Documentation.

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