Using foreach to create a for loop and dir to exctract the directory from a path with make (CC048)

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GNU Make is a great tool for insuring the reproducibility of a data analysis pipeline. We've used it in previous episodes. In this episode of Code Club, Pat Schloss will show how to create for loops and extract the directory from a path to generate a long lists of targets in our makefile. This episode is part of a larger arc of episodes investigating the sensitivity and specificity of amplicon sequence variants (ASVs), also known as exact sequence variants (ESVs). ASVs are growing in popularity for analyzing microbial communities using 16S rRNA gene sequences. Pat demonstrates these concepts by live coding at the command line interface using RStudio, GitHub Flow, and make.

0:00 Introduction
2:24 Defining and using variables
6:12 Extracting the directory from a path
9:32 For loops
13:41 Nested for loops
17:53 Building all of the targets with one line
21:04 Conclusion

  1. Riffomonas Project
  2. asv
  3. esv
  4. code club
  5. live code
  6. screencast
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Thank you so much! Your video helped me 😀

olegrubel