{"id":25977310,"url":"https://github.com/nbisweden/workshop-r","last_synced_at":"2026-03-05T16:17:46.879Z","repository":{"id":69029757,"uuid":"149093253","full_name":"NBISweden/workshop-r","owner":"NBISweden","description":"Workshop • R Programming Foundations for Life Scientists • 5 days","archived":false,"fork":false,"pushed_at":"2024-10-29T13:28:03.000Z","size":300335,"stargazers_count":7,"open_issues_count":0,"forks_count":10,"subscribers_count":41,"default_branch":"master","last_synced_at":"2024-10-29T15:14:36.776Z","etag":null,"topics":["life-scientists","r","r-programming","workshop"],"latest_commit_sha":null,"homepage":"https://nbisweden.github.io/workshop-r","language":"CSS","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/NBISweden.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-09-17T08:28:46.000Z","updated_at":"2024-10-29T13:24:09.000Z","dependencies_parsed_at":null,"dependency_job_id":"adaa1fcf-7b31-4012-aa76-6ff3feee0731","html_url":"https://github.com/NBISweden/workshop-r","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NBISweden%2Fworkshop-r","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NBISweden%2Fworkshop-r/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NBISweden%2Fworkshop-r/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/NBISweden%2Fworkshop-r/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/NBISweden","download_url":"https://codeload.github.com/NBISweden/workshop-r/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241966866,"owners_count":20050322,"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":["life-scientists","r","r-programming","workshop"],"created_at":"2025-03-05T04:33:13.134Z","updated_at":"2026-03-05T16:17:46.859Z","avatar_url":"https://github.com/NBISweden.png","language":"CSS","readme":"# workshop-r [![gh-actions-build-status](https://github.com/nbisweden/workshop-r/workflows/build/badge.svg)](https://github.com/nbisweden/workshop-r/actions?workflow=build)\n\nThis repo contains the course material for NBIS workshop **R Programming Foundation for Life Scientists**. The rendered view of this repo is available [here](https://nbisweden.github.io/workshop-r/).\n\n## Contributing\n\nTo add or update contents of this repo (for collaborators), first clone the repo.\n\n```\ngit clone https://github.com/nbisweden/workshop-r.git\n```\n\nCreate a new branch. Make changes/updates as needed. Add the changed files. Commit it. Then push the repo back.\n\n```\ngit add .\ngit commit -m \"I did this and that\"\ngit push origin\n```\n\nIf you are not added as a collaborator, first fork this repo to your account, then clone it locally, make changes, commit, push to your repo, then submit a pull request to this repo/master branch.\n\n:exclamation: When updating repo for a new course, change `output_dir: XXXX` in `_site.yml` as the first thing, so that old rendered files are not overwritten.\n\n:exclamation: Do not push any rendered .html files or intermediates.\n\n## Repo organisation\n\nThe source material is located on the *master* branch (default). The rendered material is located on the *gh-pages* branch. For most part, one only needs to update content in master. Changes pushed to the *master* branch is automatically rendered to the *gh-pages* branch.\n\nFor more details about repo organisation, updating and modifying this repo, check out the [template repo](https://github.com/royfrancis/workshop-template-rmd-ga).\n\n### Schedule\n\nSchedule is saved into the `schedule.csv` file. It is a csv file with semi-colon as delimiter. You should NOT try to edit it in a text editor, but use proper spreadsheet.\nIf you are using command line, you can install `vd` and open and edit the file `vd --csv-delimiter ';' schedule.csv`.\n\n### Docker\n\nR packages needed to build the website and run the labs are all contained in a Docker container. To run docker container locally, follow instructions below:\n\n:exclamation: Image is about 4.8 GB!\n\n```\n# pull the container\ndocker pull --platform=linux/amd64 ghcr.io/nbisweden/workshop-r:latest\n\n# render whole website\ndocker run --platform=linux/amd64 --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-r:latest Rscript -e 'rmarkdown::render_site()'\n\n# render one file\ndocker run --platform=linux/amd64 --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-r:latest Rscript -e 'rmarkdown::render(\"index.Rmd\")'\n```\n\nTo run RStudio server and develop in the browser, run;\n\n```\ndocker run --platform=linux/amd64 --rm -e PASSWORD=rstudio -p 8788:8787 -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-r:latest\n```\n\nGo to [http://localhost:8788/](http://localhost:8788/) or [http://0.0.0.0:8788](http://0.0.0.0:8788). Username is `rstudio` and password is `rstudio`. Change to folder `/rmd` to see your files.\n\nTo add new packages, you need to update `Dockerfile`, rebuild the container, test it and push it to repository. Make changes to the `Dockerfile` as needed. Then to rebuild and push the docker image, follow the steps below:\n\n:exclamation: Remember to update the version number\n:exclamation: Remember to render the whole website to make sure everything works\n\n```\n# build container and add tags\ndocker build --platform=linux/amd64 -t ghcr.io/nbisweden/workshop-r:1.1.2 .\ndocker tag ghcr.io/nbisweden/workshop-r:1.1.2 ghcr.io/nbisweden/workshop-r:latest\n\n# push to ghcr\ndocker login ghcr.io\ndocker push ghcr.io/nbisweden/workshop-r:1.1.2\ndocker push ghcr.io/nbisweden/workshop-r:latest\n```\n\n---\n\n**2025** NBIS • SciLifeLab\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnbisweden%2Fworkshop-r","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnbisweden%2Fworkshop-r","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnbisweden%2Fworkshop-r/lists"}