Tibanna runs portable pipelines (in CWL/WDL) on the AWS Cloud.
Project description
Tibanna
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.
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>
totibanna <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.
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