Using wget, unzip, tar and gunzip to download data: automate downloads from the command line (CC016)

In this screencast tutorial, Pat Schloss shows how you can use command line tools including wget, unzip, tar, and gunzip to obtain files from the internet without using a browser. Automating the download of a reference alignment and files from the rrnDB will allow us to better document our analysis and make it more reproducible. These files will be critical 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).

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/2020-07-13-downloading-data.

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