Bioinformatics and Genomics

Docker is the most common containerization software; it is used widely in both industry and scientific settings to control the computational environment in which software and data pipelines are built. In academic settings Docker is one way to increase the computational reproducibility of your work.

• Install Docker and read through the getting started pages for Mac or Windows.
• Skim this conceptual introduction and this slightly deeper dive into containers and virtual machines.
• Read about Docker for Reproducibility: https://dl.acm.org/citation.cfm?doid=2723872.2723882
• If time allows, poke around in the generic getting started docs.

Singularity is used when tighter security is needed in a server environment and for all High Performance Computing.

Nextflow is open-source software that enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. Nextflow is developed by the Comparative Bioinformatics group at the Barcelona Centre for Genomic Regulation (CRG).