/tibanna

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

Primary LanguagePythonMIT LicenseMIT

Tibanna

Python 3.8 Build Status Code Quality Test Coverage Documentation Status

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.