DockerBIO: web application for efficient use of bioinformatics Docker images

PeerJ

article

ChangHyuk Kwon¹  Jason Kim²  Jaegyoon Ahn¹ 

[1] Department of Computer Science and Engineering, Incheon National University, Incheon;MyGenomeBox, Co, Incheon

关键词: Docker;    NGS pipeline;    Dockerbio;    RNA-Seq;    DNA-Seq;    RNA pipeline;    DNA pipeline;    Bioinformatics;    Mygenomebox;   

DOI  :  10.7717/peerj.5954

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Background and Objective Docker is a light containerization program that shows almost the same performance as a local environment. Recently, many bioinformatics tools have been distributed as Docker images that include complex settings such as libraries, configurations, and data if needed, as well as the actual tools. Users can simply download and run them without making the effort to compile and configure them, and can obtain reproducible results. In spite of these advantages, several problems remain. First, there is a lack of clear standards for distribution of Docker images, and the Docker Hub often provides multiple images with the same objective but different uses. For these reasons, it can be difficult for users to learn how to select and use them. Second, Docker images are often not suitable as a component of a pipeline, because many of them include big data. Moreover, a group of users can have difficulties when sharing a pipeline composed of Docker images. Users of a group may modify scripts or use different versions of the data, which causes inconsistent results. Methods and Results To handle the problems described above, we developed a Java web application, DockerBIO, which provides reliable, verified, light-weight Docker images for various bioinformatics tools and for various kinds of reference data. With DockerBIO, users can easily build a pipeline with tools and data registered at DockerBIO, and if necessary, users can easily register new tools or data. Built pipelines are registered in DockerBIO, which provides an efficient running environment for the pipelines registered at DockerBIO. This enables user groups to run their pipelines without expending much effort to copy and modify them.

【 授权许可】

CC BY