KnowEnG's Pipelines Library
This repository provides Python scripts to support Knowledge Engine for Genomics (KnowEnG) pipelines, an NIH BD2K Center of Excellence.
There are four modules that one can choose from:
| Modules | Description |
|---|---|
| toolbox.py | Contains basic computation functions for all pipelines |
| data_cleanup_toolbox.py | Contains functions for data_cleanup_pipeline |
| distributed_computing_utils.py | Contains functions for parallel computing and distribute computing |
| redis_utilities.py | Contains API to call redis database |
How to build library: knpackage
1. Setup configuration on your machine
Follow (steps to create the scaffolding) before push your package from your machine.
2. Push packages to PyPI
Follow (steps to push package to PyPI repository) to push your package from your machine.
Note: knpackage doesn't contain any source code. It provides the necessary basic package dependencies to run KnowEnG pipeline.
How to use this library
1. Install python3-pip in your local machine
apt-get install python3-pip
3. Install knpackage in your local machine
pip3 install knpackage
2. Import modules from knpackage in your Python script
import knpackage.<module_name>
