Tibanna：用于在云端可扩展执行可移植管道的软件。
Tibanna: software for scalable execution of portable pipelines on the cloud.
机构信息
Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
出版信息
Bioinformatics. 2019 Nov 1;35(21):4424-4426. doi: 10.1093/bioinformatics/btz379.
SUMMARY
We introduce Tibanna, an open-source software tool for automated execution of bioinformatics pipelines on Amazon Web Services (AWS). Tibanna accepts reproducible and portable pipeline standards including Common Workflow Language (CWL), Workflow Description Language (WDL) and Docker. It adopts a strategy of isolation and optimization of individual executions, combined with a serverless scheduling approach. Pipelines are executed and monitored using local commands or the Python Application Programming Interface (API) and cloud configuration is automatically handled. Tibanna is well suited for projects with a range of computational requirements, including those with large and widely fluctuating loads. Notably, it has been used to process terabytes of data for the 4D Nucleome (4DN) Network.
AVAILABILITY AND IMPLEMENTATION
Source code is available on GitHub at https://github.com/4dn-dcic/tibanna.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
我们介绍了 Tibanna，这是一个开源软件工具，用于在亚马逊网络服务（AWS）上自动执行生物信息学管道。Tibanna 接受可重复和可移植的管道标准，包括通用工作流程语言（CWL）、工作流程描述语言（WDL）和 Docker。它采用了隔离和优化各个执行的策略，结合了无服务器调度方法。管道使用本地命令或 Python 应用程序编程接口（API）执行和监控，并且自动处理云配置。Tibanna 非常适合具有各种计算要求的项目，包括那些具有大量和广泛波动负载的项目。值得注意的是，它已被用于处理 4D Nucleome（4DN）网络的 TB 级数据。
可用性和实现
源代码可在 GitHub 上获得，网址为 https://github.com/4dn-dcic/tibanna。
补充信息
补充数据可在 Bioinformatics 在线获得。
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