railroadtracks is a Python toolkit to handle graphs of dependent tasks such as the ones found in bioinformatics pipelines.
It was created for comparing RNA-Seq pipelines and found its use is other situations, such as writing a flexible system for the QC of NGS data.GitHub repo
railroadtracks provides the following main features:
- ad hoc creation of pipelines, interactive use in mind and ipython-specify display of objects
- separation of the declaration of tasks from their execution
- simple abstractions to perform parallel computing allowing computations to be moved easily to different models for parallel and distributed computing
- a fully-extendable and editable model layer unifying popular tools in DNA and RNA-sequencing data processing under one common interface.
- It can be installed as a regular Python package, for example using
pip install. A tutorial as an ipython notebook is avaible as part of the documentation for the package.
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