What if reviewer number 2 tells you that it is impossible to reproduce your results? Oops! Figuring out all software versions and dependencies in your system and in the reviewer's system and compare them sounds like very tedious work! Wouldn't it be nice to send him/her your pipeline as a Docker image, with the needed software preinstalled and all the dependencies in place?
If you built a workflow for your analysis that uses different bioinformatics tools, each of these tools may have specific version requirements. By creating a Docker image with all these tools preinstalled, you can ensure that your pipeline runs in any machine (laptop, HPC or cloud). You can also share this image with your collaborators, or reviewer number 2, to ensure reproducibility of the results. Furthermore, your pipeline can more easily be deployed on the cloud.
Docker improves bioinformatics workflows by ensuring reproducibility and portability, which makes it essential in computational biology.
- What is Docker and why is it needed
- How to install it - Requirements, best practices
- Creating your first Dockerfile and adding some software (rnaseq realeted)
- File system mounts
- Build Docker images and interact with containers
- Share your Docker images (registries, Docker Hub)