tibanna


Nametibanna JSON
Version 1.2.4 PyPI version JSON
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home_pagehttp://github.com/4dn-dcic/tibanna
SummaryTibanna runs portable pipelines (in CWL/WDL) on the AWS Cloud.
upload_time2021-05-07 18:54:12
maintainer
docs_urlNone
author4DN Team at Harvard Medical School
requires_python
licenseMIT
keywords
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls.
            # Tibanna

[![Python 3.6](https://img.shields.io/badge/python-3.6-blue.svg)](https://www.python.org/downloads/release/python-360/) [![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.

<br>

Install Tibanna.
```bash
pip install tibanna
```

<br>

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
```

<br>

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')
```

<br>

---
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**](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).




            

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    "description": "# Tibanna\n\n[![Python 3.6](https://img.shields.io/badge/python-3.6-blue.svg)](https://www.python.org/downloads/release/python-360/) [![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&amp;utm_medium=referral&amp;utm_content=4dn-dcic/tibanna&amp;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&amp;utm_medium=referral&amp;utm_content=4dn-dcic/tibanna&amp;utm_campaign=Badge_Coverage) [![Documentation Status](https://readthedocs.org/projects/tibanna/badge/?version=latest)](https://tibanna.readthedocs.io/en/latest/?badge=latest)\n\n***\n\nTibanna runs portable pipelines (in CWL/WDL/Snakemake/shell) on the AWS Cloud.\n\n<br>\n\nInstall Tibanna.\n```bash\npip install tibanna\n```\n\n<br>\n\nUse CLI to set up the cloud component and run workflow.\n```bash\n# Deploy Unicorn to the Cloud (Unicorn = serverless scheduler/resource allocator).\ntibanna deploy_unicorn --usergroup=mygroup\n\n# Run CWL/WDL workflow on the Cloud.\ntibanna run_workflow --input-json=myrun.json\n```\n\n<br>\n\nAlternatively, use Python API.\n\n```python\nfrom tibanna.core import API\n\n# Deploy Unicorn to the Cloud.\nAPI().deploy_unicorn(usergroup='mygroup')\n\n# Run CWL/WDL workflow on the Cloud.\nAPI().run_workflow(input_json='myrun.json')\n```\n\n<br>\n\n---\nNote: Starting `0.8.2`, Tibanna supports local CWL/WDL files as well as shell commands and Snakemake workflows.\n\nNote2: Python2.7 support is deprecated now (`0.7.0` or after)! Please switch to Python3.6!\n\nNote3: Starting `0.8.0`, one no longer needs to `git clone` the Tibanna repo. \n* Please switch from `invoke <command>` to `tibanna <command>`! \n* We also renovated the Python API as an inheritable class to allow development around tibanna.\n\nNote4:  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`.\n\nNore5: For more details, see Tibanna [**Documentation**](http://tibanna.readthedocs.io/en/latest).\n* Also check out our [**paper in _Bioinformatics_**](https://doi.org/10.1093/bioinformatics/btz379).\n* A preprint can also be found on [**biorxiv**](https://www.biorxiv.org/content/10.1101/440974v3).\n\n\n\n",
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