Bash scripting is an essential skill in bioinformatics that is often expected that bioinformaticians will just pickup in their careers. I think that this underestimates the difficulty of learning and applying Bash scripting.
This is a book that is meant to bring you (a budding bioinformaticist) beyond the foundational shell scripting skills learned from a shell scripting course such as the Software Carpentries Shell Course.
Specifically, it shows you a path to get started with reproducible cloud computing on the DNAnexus platform.
Our goal is to showcase the "glue" skills that help you do bioinformatics reproducibly. That includes:
- Articulate basic Cloud Computing concepts
- Leverage bash scripting and the dx-toolkit to execute jobs on the DNAnexus platform
- Execute batch processing of multiple files in a project on the DNAnexus platform
- Monitor, profile, and retry jobs to optimize costs
- Manage software dependencies reproducibly using container-based technologies such as Docker
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
