pypipe

Bioinformatics pipelines framework, writen in python2.

Requirements

• python2
• setuptools
• graphviz
• PyQt4 - If you want use GUI

Instalation

$ git clone https://github.com/semkagtn/pypipe.git
$ cd pypipe/pypipe-core
$ python2 setup.py build
$ sudo python2 setup.py install

FAQ

• Installation for current user only: ./setup.py install --user
• How to write pipelines: see example.py
• How to add support of new tool: see pypipe/tools/* files
• How to create pipeline: ./pypipe.py create example.py pipeline
• How to draw pipeline to img: ./pypipe.py draw pipeline img.svg
• How to run pipeline: ./pypipe.py run-all pipeline