nuest / ten-simple-rules-dockerfiles

Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science

Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science

The manuscript is published as a preprint: https://osf.io/fsd7t

We welcome your feedback, e.g., by opening issues on this repository or with OSF annotations. We especially welcome your help by creating strong illustrating examples, see issue #4.

Ten Simple Rules Collection on PLOS

Current draft as PDF

Author contributions

DN conceived the idea and contributed to conceptualisation, methodology, and writing - original draft, review & editing, and validation. VS contributed to conceptualisation, methodology, and writing - original draft, and review & editing. BM contributed to writing – review & editing. SJE contributed to conceptualisation, writing – review & editing, and validation. THe contributed to conceptualisation. THi contributed to writing – review & editing. BDE contributed to conceptualisation, writing – review & editing, visualisation, and validation. This articles was written collaboratively on GitHub, where contributions in form of text or discussions comments are documented: https://github.com/nuest/ten-simple-rules-dockerfiles/.

Run container for editing the document

First, build the container. It will install the dependencies that you need for compiling the LaTex.

docker build -t ten-simple-rules-dockerfiles .

Then run it! You'll need to set a password to login with user "rstudio."

PASSWORD=simple
docker run --rm -it -p 8787:8787 -e PASSWORD=$PASSWORD -v $(pwd):/home/rstudio/ten-simple-rules-dockerfiles ten-simple-rules-dockerfiles

Open http://localhost:8787 to get to RStudio, log in, and navigate to the directory ~/ten-simple-rules-dockerfiles to open the Rmd file and start editing. Use the "Knit" button to render the PDF. The first rendering takes a bit longer, because required LaTeX packages must be installed.

See more options in the Rocker docs.

Run container for building the PDF

See the end of the Dockerfile for instructions.

Useful snippets

• Get all author's GitHub handles:

  cat *.Rmd | grep ' # https://github.com/' | sed 's|    # https://github.com/|@|'

• Get all author's emails:

  cat *.Rmd | grep 'email:' | sed 's|    email: ||'

• [Work in progress!] Get a .docx file out of the Rmd so one can compare versions and generate marked-up copies of changes:

  # https://github.com/davidgohel/officedown
  library("officedown")
  rmarkdown::render("ten-simple-rules-dockerfiles.Rmd", output_format = officedown::rdocx_document(), output_file = "tsrd.docx")
  
  # https://noamross.github.io/redoc/articles/mixed-workflows-with-redoc.html
  library("redoc")
  rmarkdown::render("ten-simple-rules-dockerfiles.Rmd", output_format = redoc::redoc(), output_file = "tsrd.docx")

• Compare with latexdiff

  # get a specific version of the text file
  wget -O submission.v2.tex https://raw.githubusercontent.com/nuest/ten-simple-rules-dockerfiles/submission.v2/ten-simple-rules-dockerfiles.tex
  # compare it with current version
  latexdiff --graphics-markup=2 submission.v2.tex ten-simple-rules-dockerfiles.tex > diff.tex
  # render diff.tex with RStudio

License

This manuscript is published under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, see file LICENSE.md.