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intro update
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nsheff committed Jul 2, 2016
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Expand Up @@ -5,6 +5,9 @@ Introduction
Overview
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Pypiper is a lightweight python toolkit for gluing together restartable, robust
command line pipelines. With Pypiper, simplicity is paramount. A new user can start building pipelines using Pypiper in under 15 minutes. Learning all the :doc:`features and benefits <features>` of Pypiper takes just an hour or two. At the same time, Pypiper provides immediate and significant advantages over a simple shell script.

The target user of Pypiper is a computational scientist comfortable on the command line, who has something like a bash script that would benefit from a layer of "handling code". Pypiper helps you convert that set of shell commands into a production-scale workflow, automatically handling the annoying details (restartablilty, file integrity, logging) to make your pipeline robust and restartable, with minimal learning curve.

Pypiper does not handle any sort of cluster job submission, resource requesting, or parallel dependency management (other than node-threaded parallelism inherent in your commands) -- we use `Looper <http://looper.readthedocs.io/>`_ for that (but you can use whatever you want). Pypiper just handles a one-sample, sequential pipeline, but now it's robust, restartable, and logged. When coupled with `Looper <http://looper.readthedocs.io/>`_ you get a complete pipeline management system.
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