https://github.com/nuest/ten-simple-rules-dockerfiles
Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science
https://github.com/nuest/ten-simple-rules-dockerfiles
containerisation containerization dockerfiles open-science reproducible-paper reproducible-research reproducible-science ten-simple-rules
Last synced: 6 days ago
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Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science
- Host: GitHub
- URL: https://github.com/nuest/ten-simple-rules-dockerfiles
- Owner: nuest
- License: cc-by-4.0
- Created: 2019-05-31T15:37:13.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2020-11-11T09:04:54.000Z (over 4 years ago)
- Last Synced: 2025-04-02T01:49:36.498Z (13 days ago)
- Topics: containerisation, containerization, dockerfiles, open-science, reproducible-paper, reproducible-research, reproducible-science, ten-simple-rules
- Language: TeX
- Homepage: https://doi.org/10.1371/journal.pcbi.1008316
- Size: 19.6 MB
- Stars: 65
- Watchers: 8
- Forks: 15
- Open Issues: 18
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
# Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science
[](https://doi.org/10.1371/journal.pcbi.1008316)
[](https://doi.org/10.31219/osf.io/fsd7t)
The manuscript is published as a preprint: **[https://osf.io/fsd7t](https://osf.io/fsd7t)**
We welcome your feedback, e.g., by opening issues on this repository or with [OSF annotations](https://help.osf.io/hc/en-us/articles/360019738554-Annotate-a-Preprint).
We especially welcome your help by creating strong illustrating examples, see [issue #4](https://github.com/nuest/ten-simple-rules-dockerfiles/issues/4).
[Ten Simple Rules Collection on PLOS](https://collections.plos.org/ten-simple-rules)
[Current draft as PDF](https://nuest.github.io/ten-simple-rules-dockerfiles/ten-simple-rules-dockerfiles.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](https://github.com/nuest/ten-simple-rules-dockerfiles/graphs/contributors) are documented: [https://github.com/nuest/ten-simple-rules-dockerfiles/](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.
```bash
docker build -t ten-simple-rules-dockerfiles .
```
Then run it! You'll need to set a password to login with user "rstudio."
```bash
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](https://github.com/rocker-org/rocker-versioned/blob/master/rstudio/README.md#additional-configuration-options).
## Run container for building the PDF
See the end of the `Dockerfile` for instructions.
## Useful snippets
- Get all author's GitHub handles:
```bash
cat *.Rmd | grep ' # https://github.com/' | sed 's| # https://github.com/|@|'
```
- Get all author's emails:
```bash
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:
```r
# 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`
```bash
# 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](https://creativecommons.org/licenses/by/4.0/) (CC BY 4.0) license, see file [LICENSE.md](LICENSE.md).