Aliases and a custom prompt: tools that can facilitate reproducibility (CC025)
Channel: Riffomonas Project
Date: 2020-08-13

In this screencast tutorial, Pat Schloss shows how you can customize the behavior of your command line interface to facilitate your analysis and ultimately make it more reproducible. We will create aliases and customized prompts by modifying the bashrc and bash_profiles that live in your home directory. He also discusses how some customizations can hinder reproducibility. Considering the amount of time we spend in the command line, it's important to have things configured to maximize our comfort. These little changes will be important as we determine the degree to which inter- and intra-genomic variation limit the interpretation of amplicon sequence variants (ASVs; aka exact sequence variants or ESVs) for different regions within the 16S rRNA gene. This is an important question for microbiome researchers.

Pat demonstrates these concepts by live coding at the command line interface using RStudio, GitHub Flow, and make. He then turns viewers loose to work through several activities to answer related questions and finishes by giving his solutions.

The accompanying blog post contains the exercises and solutions can be found at http://www.riffomonas.org/code_club/2020-08-13-customizing-bash



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