pypez 0.1.5

simple pipelines in python

Overview

A simple module for specifying and executing a sequence of commands, with up to 1 level of branching (where several tasks are executed in parallel) before continuing with a single line of execution.

Features

• executes a sequences of command lines, allowing some steps to run in parallel, before proceeding sequentially again.

• save command standard output to a log file.

• use temp output files for each command until it completes successfully. Then move them to their final location.

• by default don’t rerurn steps if the output file(s) exist and are newer than the input file(s).

• run locally by default or on SGE (with –use_SGE) or LSF (with –use_LSF).