{"id":14069899,"url":"https://github.com/nuest/ten-simple-rules-dockerfiles","last_synced_at":"2025-04-09T00:05:06.887Z","repository":{"id":43288053,"uuid":"189618722","full_name":"nuest/ten-simple-rules-dockerfiles","owner":"nuest","description":"Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science","archived":false,"fork":false,"pushed_at":"2020-11-11T09:04:54.000Z","size":20506,"stargazers_count":65,"open_issues_count":18,"forks_count":15,"subscribers_count":8,"default_branch":"master","last_synced_at":"2025-04-02T01:49:36.498Z","etag":null,"topics":["containerisation","containerization","dockerfiles","open-science","reproducible-paper","reproducible-research","reproducible-science","ten-simple-rules"],"latest_commit_sha":null,"homepage":"https://doi.org/10.1371/journal.pcbi.1008316","language":"TeX","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nuest.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-05-31T15:37:13.000Z","updated_at":"2025-02-22T01:12:36.000Z","dependencies_parsed_at":"2022-09-19T05:01:30.179Z","dependency_job_id":null,"html_url":"https://github.com/nuest/ten-simple-rules-dockerfiles","commit_stats":null,"previous_names":[],"tags_count":9,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nuest%2Ften-simple-rules-dockerfiles","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nuest%2Ften-simple-rules-dockerfiles/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nuest%2Ften-simple-rules-dockerfiles/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nuest%2Ften-simple-rules-dockerfiles/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nuest","download_url":"https://codeload.github.com/nuest/ten-simple-rules-dockerfiles/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247947859,"owners_count":21023066,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["containerisation","containerization","dockerfiles","open-science","reproducible-paper","reproducible-research","reproducible-science","ten-simple-rules"],"created_at":"2024-08-13T07:07:19.228Z","updated_at":"2025-04-09T00:05:06.870Z","avatar_url":"https://github.com/nuest.png","language":"TeX","readme":"# Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science\n\n\u003cimg alt=\"Ten Simple Rules for Writing Dockerfiles for Reproducible Research - Summary\" src=\"https://raw.githubusercontent.com/nuest/ten-simple-rules-dockerfiles/master/figures/summary.png\" width=\"30%\" align=\"right\"\u003e\n\n[![Article DOI](https://img.shields.io/badge/Article-10.1371%2Fjournal.pcbi.1008316-yellow)](https://doi.org/10.1371/journal.pcbi.1008316)\n\n[![Preprint DOI](https://img.shields.io/badge/Preprint-10.31219%2Fosf.io%2Ffsd7t-blue)](https://doi.org/10.31219/osf.io/fsd7t)\n\nThe manuscript is published as a preprint: **[https://osf.io/fsd7t](https://osf.io/fsd7t)**\n\nWe 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).\nWe especially welcome your help by creating strong illustrating examples, see [issue #4](https://github.com/nuest/ten-simple-rules-dockerfiles/issues/4).\n\n[Ten Simple Rules Collection on PLOS](https://collections.plos.org/ten-simple-rules)\n\n[Current draft as PDF](https://nuest.github.io/ten-simple-rules-dockerfiles/ten-simple-rules-dockerfiles.pdf)\n\n## Author contributions\n\u003c!--PLOS asked to remove this from the manuscript--\u003e\n\nDN conceived the idea and contributed to conceptualisation, methodology, and writing - original draft, review \u0026 editing, and validation.\nVS contributed to conceptualisation, methodology, and writing - original draft, and review \u0026 editing.\nBM contributed to writing – review \u0026 editing.\nSJE contributed to conceptualisation, writing – review \u0026 editing, and validation.\nTHe contributed to conceptualisation.\nTHi contributed to writing – review \u0026 editing.\nBDE contributed to conceptualisation, writing – review \u0026 editing, visualisation, and validation.\nThis 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/).\n\n## Run container for editing the document\n\nFirst, build the container. It will install the dependencies that you\nneed for compiling the LaTex.\n\n```bash\ndocker build -t ten-simple-rules-dockerfiles .\n```\n\nThen run it! You'll need to set a password to login with user \"rstudio.\"\n\n```bash\nPASSWORD=simple\ndocker run --rm -it -p 8787:8787 -e PASSWORD=$PASSWORD -v $(pwd):/home/rstudio/ten-simple-rules-dockerfiles ten-simple-rules-dockerfiles\n```\n\nOpen 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.\nUse the \"Knit\" button to render the PDF.\nThe first rendering takes a bit longer, because required LaTeX packages must be installed.\n\nSee more options [in the Rocker docs](https://github.com/rocker-org/rocker-versioned/blob/master/rstudio/README.md#additional-configuration-options).\n\n## Run container for building the PDF\n\nSee the end of the `Dockerfile` for instructions.\n\n## Useful snippets\n\n- Get all author's GitHub handles:\n  ```bash\n  cat *.Rmd | grep ' # https://github.com/' | sed 's|    # https://github.com/|@|'\n  ```\n- Get all author's emails:\n  ```bash\n  cat *.Rmd | grep 'email:' | sed 's|    email: ||'\n  ```\n- [Work in progress!] Get a `.docx` file out of the Rmd so one can compare versions and generate marked-up copies of changes:\n  ```r\n  # https://github.com/davidgohel/officedown\n  library(\"officedown\")\n  rmarkdown::render(\"ten-simple-rules-dockerfiles.Rmd\", output_format = officedown::rdocx_document(), output_file = \"tsrd.docx\")\n  \n  # https://noamross.github.io/redoc/articles/mixed-workflows-with-redoc.html\n  library(\"redoc\")\n  rmarkdown::render(\"ten-simple-rules-dockerfiles.Rmd\", output_format = redoc::redoc(), output_file = \"tsrd.docx\")\n  ```\n- Compare with `latexdiff`\n  ```bash\n  # get a specific version of the text file\n  wget -O submission.v2.tex https://raw.githubusercontent.com/nuest/ten-simple-rules-dockerfiles/submission.v2/ten-simple-rules-dockerfiles.tex\n  # compare it with current version\n  latexdiff --graphics-markup=2 submission.v2.tex ten-simple-rules-dockerfiles.tex \u003e diff.tex\n  # render diff.tex with RStudio\n  ```\n\n## License\n\nThis 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).\n","funding_links":[],"categories":["TeX"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnuest%2Ften-simple-rules-dockerfiles","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnuest%2Ften-simple-rules-dockerfiles","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnuest%2Ften-simple-rules-dockerfiles/lists"}