Abstract
Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and to promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, government sources, and private owners in the Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker. The present workflow enables analysis and visualization of pan-genomes and biosynthetic gene clusters of bacteria. This provides a new solution for bioinformatics mining of big data from various publicly available biological databases. The present step-by-step guide creates an integrative workflow through a Dockerfile to allow researchers to build their own Image and run Container easily.
Highlights
Docker is an open source project and platform for building, shipping, and running any app, enabling the widespread distribution of applications
Fast and reproducible building of the BGDMdocker workflow across computing platforms using Docker Using Docker technology, the Dockerfile script file can build Images and run a container in seconds or milliseconds on Linux and Windows
We present a BGDMdocker workflow to achieve bacterial and viral genome annotation, pan-genome analysis, mining of biosynthetic gene clusters, and visualization of results on a local host or online. This allows researchers to browse information for every gene, including duplication, diversity, indel events, and sequence alignments, as well as for biosynthetic gene clusters, including structure, type, description, detailed annotation, and predicted core structure of the target compounds. These tools and their installation commands and dependencies were all written in a Dockerfile
Summary
Docker is an open source project and platform for building, shipping, and running any app, enabling the widespread distribution of applications. Docker allows users to package an application, along with all its dependencies, into a standardized unit for software development (https://docs.docker.com/). Docker includes three core structural compositions: Image, Container, and Repository. When an app is in Docker containers, setting up and maintaining different environments or tools for each language is not necessary (https://hub.docker.com/). The Docker Hub Registry allows users to find, manage, and pull Images from community, official, and private image libraries, and is free to use for public repositories (https://www.docker.com/whatisdocker). GitHub is a web-based source code version control repository and Internet hosting service that is mostly used for code. Compared with GitHub, Docker Hub (https://hub.docker.com/) is a cloud-based registry service of Docker, whose most notable advantages include workflow automation throughout the development pipeline based on Images and Counter of Docker
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