Overview

Tibanna is a software tool that helps you run genomic pipelines on the the Amazon (AWS) cloud. It is also used by 4DN-DCIC (4D Nucleome Data Coordination and Integration Center) to process data.

_images/tibanna_v6.png

What do I need to run pipelines using Tibanna?

  • Your pipeline
  • Your data
  • An Amazon Web Services (AWS) cloud account
  • Tibanna

Pipeline

  • The commands to run your pipeline must be written in either Common Workflow Language (CWL) (recommended), Workflow Description Language (WDL) (only basic support), Snakemake or a list of shell commands.
  • The pipelines may be local CWL/WDL/Snakemake files or they should be downloadable from public urls.
  • With the exception of Snakemake, your pipeline and dependencies must be pre-installed as a Docker image (https://www.docker.com/). For Snakemake, conda can be used instead.

Data

  • Your data must be in AWS S3 buckets.

AWS cloud account

  • Confirm that you can log in to AWS.

Tibanna

  • Tibanna is open-source and can be found on github.
  • Once installed, Tibanna can be run either as a set of commend-line tools or a set of python modules.

Command-line tools

$ tibanna run_workflow --input-json=run1.json

Python

>>> from tibanna.core import API
>>> API().run_workflow(input_json='run1.json')  # input_json is a json file or a dict object

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