Containerization for Reproducible Bioinformatics Research
As computational work becomes increasingly embedded in biomedical research practices, computational reproducibility has become an issue of increasing importance. Computational reproducibility requires that other researchers are able to deploy and use software and analysis workflows in their own computing environments. Platforms like Docker and Singularity allow the creation and configuration of software containers, which can be distributed and deployed across a range of systems. This lecture, presented by Steve Tsang, will give an introductory overview of containerization and how containers can facilitate reproducible bioinformatics research, providing examples from the NCI Cloud Resources and various hackathons.
Recording - https://youtu.be/gQ2PcxyzW7s
GitHub - https://github.com/stevetsa/nlmreproducibility
Slides - https://docs.google.com/presentation/d/16f8_z6tlULBc9nXLghCp04TGyVlZzKzazUNbdprROhs/edit
click to select slides.ipynb
Install Docker in your environment
git clone https://github.com/stevetsa/nlmreproducibility.git
docker run -v `pwd`:`pwd` -w `pwd` -i -t -p 8888:8888 stevetsa/nlmreproducibility
## inside container - follow on screen instructions (Copy/paste this URL/token into your browser )
## click to select the nlmreproducibility folder
## click to select slides.ipynb