Specifying package dependency in a bioinformatics project (not an R package)


#1

I develop a bioinformatics project in rstudio, which consists of some drivers script to generate data and rmd files for summarizing results. When someone check out my project to reproduce my analyses. I want them to be able to install all the package the project depends on easily.

Do I specify dependencies as if it's a "package" using DESCRIPTION.txt (http://r-pkgs.had.co.nz/description.html#dependencies)

Or is there another way to do this?


#2

There's no standard way to do this outside of a package. I suggest making a README.md file which describes

  • What the project is
  • Required packages
  • Other required software, if any
  • How to run the analysis

As a bonus, these types of files are incredibly useful when revisiting older projects. I make them even for projects I never expect to share.


#3

Thank you for the suggestion. I also thought about using putting it in a docker container but I think a README.md will do for now.


#4

You might also look at Packrat, it might be heavier than what you want but it will help with your package dependency worries.

Not my answer but this might be a good reference for you: