{"id":19624205,"url":"https://github.com/bioconductor/biocworkshops2019","last_synced_at":"2025-02-26T19:34:56.956Z","repository":{"id":136334743,"uuid":"184774812","full_name":"Bioconductor/BiocWorkshops2019","owner":"Bioconductor","description":"The official repository of the Bioconductor 2019 Conference Workshops :confetti_ball:","archived":false,"fork":false,"pushed_at":"2023-03-15T21:05:13.000Z","size":175642,"stargazers_count":25,"open_issues_count":34,"forks_count":15,"subscribers_count":15,"default_branch":"devel","last_synced_at":"2025-01-09T11:58:12.048Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://bioconductor.github.io/BiocWorkshops2019/","language":"Dockerfile","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Bioconductor.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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":"2019-05-03T15:00:39.000Z","updated_at":"2023-10-20T14:57:14.000Z","dependencies_parsed_at":null,"dependency_job_id":"d1ed05ad-7061-4c1b-961d-6924f37e1343","html_url":"https://github.com/Bioconductor/BiocWorkshops2019","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FBiocWorkshops2019","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FBiocWorkshops2019/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FBiocWorkshops2019/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2FBiocWorkshops2019/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Bioconductor","download_url":"https://codeload.github.com/Bioconductor/BiocWorkshops2019/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240922946,"owners_count":19879199,"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":[],"created_at":"2024-11-11T11:37:16.320Z","updated_at":"2025-02-26T19:34:56.922Z","avatar_url":"https://github.com/Bioconductor.png","language":"Dockerfile","funding_links":[],"categories":[],"sub_categories":[],"readme":"\nThis repository contains details of the build process and usage for materials\nfrom the [Bioc2019 conference].\n\n[Bioc2019 conference]: https://bioc2019.bioconductor.org\n\n# Compiled Workshops Link\n\nhttps://rebrand.ly/biocworkshops2019\n\n# Running workshop materials locally\n\nThe workshops (except the CWL workshop) are all installed and\nready-to-run inside [docker]; you will need to *install docker* on your machine to\nfollow along. We have a base docker image [seandavi/bioc_2019] that contains\nthe operating system and base R installation. The workshops and additional package (over 600)\nare included as a separate download that can be mounted into the container\nas a `volume`. To use the entire set of workshop materials, do:\n\n- Make a directory for the installed packages:\n\n    ```\n    mkdir /home/ubuntu/bioc-libs # or another convenient directory with about 20GB of free space\n    ```\n\n- Download and untar entire tar.gz file with all installed packages and materials:\n\n    ```\n    cd /home/ubuntu/bioc-libs # use the directory from above\n    wget https://s3.amazonaws.com/biocbuild.cancerdatasci.org/bioc2019-usr-local.tar.gz\n    tar -xzf bioc2019-usr-local.tar.gz\n    ```\n\n- Run docker locally with (you may or may not need `sudo` depending on your docker setup):\n\n    ```\n    # again, use the directory from above\n    sudo docker run --name bioc_2019 -d -v /home/ubuntu/bioc-libs:/usr/local/lib/R/site-library \\\n        -p 80:8787 -e PASSWORD=bioc seandavi/bioc_2019\n    ```\n\n- Credentials:\n  - username: 'rstudio'\n  - password: 'as you set it--bioc above'\n\n[docker]: https://docker.io\n[seandavi/bioc_2019]: https://cloud.docker.com/u/seandavi/repository/docker/seandavi/bioc_2019\n\n\n# Instructions For Workshop Authors\n\n## Getting started\n\nTo contribute a new workshop, open a [BiocWorkshops issue][] starting with\nthe `[Workshop]` keyword in the title of the issue. Provide a link to the\nrepository in the issue message body. You may also include GitHub usernames\nof workshop collaborators. For a successful workshop build, adhere to the\nfollowing:\n\n1. Package your workshop as an R package. The example package https://github.com/lpantano/dummychapter1 demonstrates all key elements of how your package must be prepared, and also provides an example `.travis.yml` for Continuous Integration against bioc-devel.\n2. Include a standard vignette in the vignettes directory\n3. Put any extra files (images, .bib) in `inst/vignettes` and reference them\nin the vignette using `system.file`\n4. Number **3** requires package chapter installation before vignette build or\n`build_vignettes=TRUE` when building the package.\n5. Use only one top-level section (`#`), for the title of your workshop. All other sections must be second-level (`##`) or lower. You may find the [usage section of the Bookdown documentation](https://bookdown.org/yihui/bookdown/usage.html) helpful for background.\n6. Do not use `BiocStyle` functionality. The style will be based on bookdown/gitbook.\n\n### DESCRIPTION\n\nUpdate the DESCRIPTION file adding packages utilized in your workshop to\nthe **Imports** field.\n\n### Use bioc-devel\n\nBioC2019 workshops will run on **bioc-devel (3.10)**. That means that this book will be built on bioc-devel, workshop participants will use virtual machines running bioc-devel, and your workshops will be tested against bioc-devel. See [Using ‘bioc-devel’ during mid-April to mid-October](https://www.bioconductor.org/developers/how-to/useDevel/) for how to run bioc-devel; thankfully we are in the easy time of year for running release and devel side-by-side. Also, the [dummy chapter](https://github.com/lpantano/dummychapter1) includes a highly recommendable TravisCI setup for Continuous Integration against bioc-devel.\n\n## Deadlines for Bioc2019\n\nPlease be aware of the following deadlines for the [Bioconductor 2019 Conference][] in New York\n\n- **Mon May 27:** draft workshop materials submitted as an Issue to this Bioconductor GitHub repo\n- **Mon June 10:** complete workshop submitted. Only bugfixes / refinements should be made after this point.\n- **Mon June 17:** All workshops complete and building without error. No new commits to contributor repos will be incorporated.\n\n[BiocWorkshops issue]: https://github.com/Bioconductor/BiocWorkshops2019/issues\n[Bioconductor 2019 Conference]: https://bioc2019.bioconductor.org/\n\n\u003ca rel=\"license\" href=\"http://creativecommons.org/licenses/by/4.0/\"\u003e\u003cimg alt=\"Creative Commons License\" style=\"border-width:0\" src=\"https://i.creativecommons.org/l/by/4.0/88x31.png\" /\u003e\u003c/a\u003e\u003cbr /\u003eThis work is licensed under a \u003ca rel=\"license\" href=\"http://creativecommons.org/licenses/by/4.0/\"\u003eCreative Commons Attribution 4.0 International License\u003c/a\u003e.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fbiocworkshops2019","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioconductor%2Fbiocworkshops2019","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fbiocworkshops2019/lists"}