Railroadtracks

Project details

Released 11/7/2014

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.

Use in the ipython notebook

Model for RNA-Seq

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