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 project Download Railroadtracks Documentation (PDF)

railroadtracks is providing 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.