Taming complex bioinformatics workflows with weaver, makeflow, and starch

A. Thrasher, Rory Carmichael, Peter Bui, Li Yu, D. Thain, S. Emrich
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引用次数: 17

Abstract

In this paper we discuss challenges of common bioinformatics applications when deployed outside their initial development environments. We propose a three-tiered approach to mitigate some of these issues by leveraging an encapsulation tool, a high-level workflow language, and a portable intermediary. As a case study, we apply this approach to refactor a custom EST analysis pipeline. The Starch tool encapsulates program dependencies to simplify task specification and deployment. The Weaver language provides abstractions for distributed computing and naturally encourages code modularity. The Makeflow workflow engine provides a batch system agnostic engine to execute compiled Weaver code. To illustrate the benefits of our framework, we compare implementations, show their performance, and discuss benefits derived from our new workflow approach relative to traditional bioinformatics development.
驯服复杂的生物信息学工作流程与编织,制作流程,和淀粉
在本文中,我们讨论了在初始开发环境之外部署常见生物信息学应用程序时所面临的挑战。我们提出了一种三层方法,通过利用封装工具、高级工作流语言和可移植中介来缓解其中的一些问题。作为一个案例研究,我们应用这种方法重构自定义的EST分析管道。Starch工具封装了程序依赖项,以简化任务规范和部署。Weaver语言为分布式计算提供抽象,并自然地鼓励代码模块化。makflow工作流引擎提供了一个与批处理系统无关的引擎来执行编译后的Weaver代码。为了说明我们的框架的好处,我们比较了实现,展示了它们的性能,并讨论了相对于传统生物信息学开发,我们的新工作流方法所带来的好处。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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