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https://github.com/4dn-dcic/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.
https://github.com/4dn-dcic/tibanna

aws aws-lambda aws-step-function bioinformatics conda cwl cwl-workflow docker pipelines snakemake snakemake-workflow wdl wdl-workflow

Last synced: 1 day ago
JSON representation

Host: GitHub
URL: https://github.com/4dn-dcic/tibanna
Owner: 4dn-dcic
License: mit
Created: 2016-07-14T15:42:51.000Z (over 8 years ago)
Default Branch: master
Last Pushed: 2024-08-06T17:33:11.000Z (3 months ago)
Last Synced: 2024-08-07T17:46:08.078Z (3 months ago)
Topics: aws, aws-lambda, aws-step-function, bioinformatics, conda, cwl, cwl-workflow, docker, pipelines, snakemake, snakemake-workflow, wdl, wdl-workflow
Language: Python
Homepage:
Size: 134 MB
Stars: 70
Watchers: 15
Forks: 27
Open Issues: 26
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.rst
- Contributing: CONTRIBUTING.rst
- License: LICENSE.txt

Awesome Lists containing this project

README

        # Tibanna

[![Python 3.8](https://img.shields.io/badge/python-3.8-blue.svg)](https://www.python.org/downloads/release/python-380/) [![Build Status](https://travis-ci.org/4dn-dcic/tibanna.svg?branch=master)](https://travis-ci.org/4dn-dcic/tibanna) [![Code Quality](https://api.codacy.com/project/badge/Grade/d2946b5bc0704e5c9a4893426a7e0314)](https://www.codacy.com/app/4dn/tibanna?utm_source=github.com&utm_medium=referral&utm_content=4dn-dcic/tibanna&utm_campaign=Badge_Grade) [![Test Coverage](https://api.codacy.com/project/badge/Coverage/d2946b5bc0704e5c9a4893426a7e0314)](https://www.codacy.com/app/4dn/tibanna?utm_source=github.com&utm_medium=referral&utm_content=4dn-dcic/tibanna&utm_campaign=Badge_Coverage) [![Documentation Status](https://readthedocs.org/projects/tibanna/badge/?version=latest)](https://tibanna.readthedocs.io/en/latest/?badge=latest)

***

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




Install Tibanna.

```bash

pip install tibanna

```




Use CLI to set up the cloud component and run workflow.

```bash

# 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.

```python

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 ` to `tibanna `! 

* We also renovated the Python API as an inheritable class to allow development around tibanna.

For more details, see Tibanna [**Documentation**](http://tibanna.readthedocs.io/en/latest).

* Also check out our [**paper in _Bioinformatics_**](https://doi.org/10.1093/bioinformatics/btz379).

* A preprint can also be found on [**biorxiv**](https://www.biorxiv.org/content/10.1101/440974v3).