Bpipe: a tool for running and managing bioinformatics pipelines

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Abstract
Summary: Bpipe is a simple, dedicated programming language for defining and executing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, Bpipe is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments. Availability and implementation: Bpipe is freely available from http://bpipe.org under a BSD License. Contact:simon.sadedin@mcri.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.