Dockstore - A Platform for Sharing Tools & Workflows on the Cloud Commons

项目摘要 在互联网的所有领域，安全、监管和隐私问题加上带宽限制 正在将大数据技术从数据传输转向原位分析数据的算法。 生物医学可以利用像Docker这样的通用技术，这些技术已经发展到可以满足 这个转变。Docker已经为计算机代码提供了一个新的轻量级可移植性， 在生物信息学中有很大的渗透。最近没有一个项目能比大型国际泛 癌症全基因组分析（PCAWG，https：//dcc.icgc.org/pcawg）合作。这一努力看到了 创建通用分析管道，统一应用于超过100个国家的全基因组序列， 2，800名癌症捐赠者在14个不同的HPC和云计算环境中广泛使用Docker 集装箱技术这一努力的关键是重新思考算法的开发，包装和开发的方式。 从一个环境转移到另一个环境。最终的结果是创建了Dockstore项目 (http：dockstore.org）的示例。Dockstore促进了生物分子分析工具的共享和移动性， 工作流程。它允许生物信息学家将单个工具和整个工作流程打包在一起， 可移植Docker镜像（容器），使用通用工作流语言（CWL）或 工作流描述语言（WDL）。通过这种方式，Dockstore简化了计算分析， 它们可以在任何支持Docker的环境中精确地复制和运行。 这里提出的工作支持扩展开发、强化、内容添加、云集成 并将Dockstore传播到更广泛的生物医学研究社区。最重要的是，它支持 在全球基因组健康联盟（GA 4GH）的主持下， 通过API与全球其他类似项目一起使用Dockstore，可以搜索容器 和工作流程。联合网络将允许团体和个人项目 不仅创建单个分析，而且创建机构品牌和共享的整个分析库 在一个共同的GA 4GH指数和一套互操作性标准下与世界其他地区进行合作。结果将 成为一个集成网络，提供便携式、安全签名、易于部署的工作流程和工具，涵盖 生物医学分析的范围。它将使发现，测试和应用这些分析新的数据少得多 耗时且容易出错，并减少关键生物信息学任务的冗余重新实现。在 这与之前像Galaxy这样有影响力的努力所采取的方法形成了鲜明对比， 方法，证明难以扩展到大型数据集，重点放在便携式，可扩展的工作流标准， 可以在各种平台上运行，使其成为广泛的生物医学分析的正确基础。

Project Abstract Across all sectors of the Internet security, regulatory and privacy concerns coupled with bandwidth limitations are shifting Big Data technologies away from data transfer and toward algorithms that analyze data in situ. Biomedicine can take advantage of general technologies like Docker that have evolved to meet the needs of this shift. Already Docker, which allows a new level of lightweight portability for computer code, has significantly penetrated bioinformatics. No recent project illustrates this better than the large, international Pan Cancer Analyses of Whole Genomes (PCAWG, https://dcc.icgc.org/pcawg) collaboration. This effort saw the creation of common analytical pipelines that were uniformly applied to the whole genome sequences of over 2,800 cancer donors in 14 disparate HPC and cloud computing environments, making extensive use of Docker container technology. Critical to this effort was a rethink of the way algorithms were developed, packaged, and moved from environment to environment. The net outcome was the creation of the Dockstore project (http://dockstore.org). Dockstore facilitates the sharing and mobility of biomolecular analysis tools and workflows. It allows bioinformaticians to bring together individual tools and entire workflows packaged in portable Docker images (containers), described using either the Common Workflow Language (CWL) or Workflow Description Language (WDL). In this way, Dockstore standardizes computational analyses, making them precisely reproducible and runnable in any environment that supports Docker. The work proposed here supports the extended development, hardening, content addition, cloud integration and dissemination of the Dockstore to the wider biomedical research community. Most importantly, it supports full federation, under the auspices of the Global Alliance for Genomics Health (GA4GH), of the original Dockstore with other similar projects worldwide through an API that makes it possible to search for containers and workflows across a global network. The federated network will allow groups and individual projects to create not only individual analyses, but entire analysis repositories that are institutionally branded and shared with the rest of the world under a common GA4GH index and set of interoperability standards. The result will be an integrated network providing portable, securely signed, easily deployed workflows and tools covering the spectrum of biomedical analyses. It will make finding, testing and applying these analyses to new data far less time consuming and error prone, and reduce redundant reimplementation of key bioinformatic tasks. In contrast to the approach taken previously by influential efforts like Galaxy, which resulted in pushbutton methods that proved hard to scale to large datasets, the focus on portable, scalable workflow standards, which can be run within a variety of platforms, make this the right basis for a broad biomedical analysis commons.