{"id":19624260,"url":"https://github.com/bioconductor/bioconductor_full","last_synced_at":"2025-04-28T05:31:31.465Z","repository":{"id":146388236,"uuid":"172123737","full_name":"Bioconductor/bioconductor_full","owner":"Bioconductor","description":"DEPRECATED - Docker Images which include a complete installation of all software needed to build all Bioconductor packages","archived":false,"fork":false,"pushed_at":"2023-03-15T21:04:28.000Z","size":69,"stargazers_count":26,"open_issues_count":5,"forks_count":4,"subscribers_count":10,"default_branch":"devel","last_synced_at":"2024-05-09T07:47:29.670Z","etag":null,"topics":["bioconductor","containers","docker"],"latest_commit_sha":null,"homepage":"http://bioconductor.org/help/docker/","language":"Dockerfile","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","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":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2019-02-22T19:31:48.000Z","updated_at":"2023-03-15T21:04:33.000Z","dependencies_parsed_at":"2023-10-20T18:25:41.212Z","dependency_job_id":null,"html_url":"https://github.com/Bioconductor/bioconductor_full","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%2Fbioconductor_full","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fbioconductor_full/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fbioconductor_full/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fbioconductor_full/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Bioconductor","download_url":"https://codeload.github.com/Bioconductor/bioconductor_full/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224096932,"owners_count":17255192,"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":["bioconductor","containers","docker"],"created_at":"2024-11-11T11:37:26.402Z","updated_at":"2024-11-11T11:37:29.072Z","avatar_url":"https://github.com/Bioconductor.png","language":"Dockerfile","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Bioconductor Devel Docker image - DEPRECATED\n\n**Deprecation Notice** : The `bioconductor/bioconductor_full` images have been deprecated in favor of the new `bioconductor/bioconductor_docker` images located at https://github.com/bioconductor/bioconductor_docker . These new images will have the same functionality as `bioconductor_full`, and users should find it easy to switch between the new set of containers. Please refer to the [README.md](https://github.com/Bioconductor/bioconductor_docker/blob/master/README.md) of the new images for more information.\n\nBioconductor Docker image with full set of system dependencies so that\nall Bioconductor packages can be installed.\n\nThe Docker images have R and Bioconductor with different versions\nunder each \"branch\" in git.\n\n**NOTE**: Docker image for bioconductor_full:devel is in the `master`\nbranch, and all the release branches will be under the branch\n`RELEASE_X_Y`.\n\nImportant Links:\n\n[Docker hub link for bioconductor_full](https://hub.docker.com/r/bioconductor/bioconductor_full)\n\n[Github development link for bioconductor_full](https://github.com/Bioconductor/bioconductor_full)\n\n## Advantages of the `bioconductor_full` docker image\n\n1. The bioconductor_full docker images can be used instead of\n   installing complex dependencies needed for Bioconductor\n   packages. The image comes with most of the dependencies installed.\n\n1. Quick start up to start your analysis with all the Bioconductor\n   packages if needed.\n\n1. The image will be regularly updated to reflect the build system on\n   Bioconductor. This is a very useful resource for maintainers who\n   are actively developing their package to see if it works in tandem\n   with the bioconductor ecosystem. It provides a local testing outlet\n   for maintainers and developers.\n\n## Installation and quick start\n\nThis document assumes you have [docker][] installed. Please check\n[installation][] if you have more questions regarding this.\n\n[docker]: https://www.docker.com/\n[installation]: https://www.docker.com/products/docker-desktop\n\n### Quick start\n\n* Start docker on your machine.\n\n* On the command line, \"pull\" the bioconductor_full docker image with\n  the correct tag. These images are hosted on docker hub under the\n  [Bioconductor organization][] page.\n\n        docker pull bioconductor/bioconductor_full:devel\n\n    or\n\n        docker pull bioconductor/bioconductor_full:RELEASE_X_Y\n\n* Once the image is available on your local machine, you can check to\n  see if they are available.\n\n        docker images\n\n* To start using these images with RStudio, this will start the image\n  under the 'rstudio' user\n\n        docker run                                      \\\n            -e PASSWORD=your_password                   \\\n            -p 8787:8787                                \\\n            -v ~/host-site-library:/usr/local/lib/R/host-site-library \\\n            bioconductor/bioconductor_full:devel\n\n* To start the image interactively using the `bioc` user\n\n        docker run                                     \\\n            -it                                        \\\n            --user bioc                                \\\n            -v ~/host-site-library:/usr/local/lib/R/host-site-library \\\n            bioconductor/bioconductor_full:devel       \\\n            R\n\n    NOTE: The path `/usr/local/lib/R/host-site-library` is mapped to\n    `.libPaths()` in R. So, when R is started, all the libraries in\n    the host directory, `host-site-library` are available to R. It is\n    stored on your machine mounted from the volume you fill in place\n    of `host-site-library`.\n\n    These libraries will only work if they are pre-compiled with the\n    same version of R that is in the docker image. To explain further,\n    you would need the packages built with Bioconductor version '3.9'\n    to work with R-3.6. Similarly, you'd need Bioconductor version\n    '3.9' to work with R-3.6.z.\n\n* To start the docker image in deamon mode, i.e, have the container\n  running in the background use the `-d` option.\n\n        sudo docker run -it                            \\\n            -d                                         \\\n            -v host-site-library:/usr/local/lib/R/host-site-library \\\n            --entrypoint /bin/bash                     \\\n            bioconductor/bioconductor_full:devel\n\n  This will start the container in the background and keep it\n  running. You may check the running processes using `docker ps`,\n  and copy the container id.\n\n        docker ps\n\n  To attach to a container which is running in the background\n\n        docker exec -it \u003ccontainer_id\u003e bash\n\n  NOTE: You can replace `bash` with R to start R directly in the\n  container.\n\n        docker exec -it \u003ccontainer_id\u003e R\n\n* To run multiple RStudio instances, use a different external port\n  mapping (the first port in `-p XXXX:YYYY`) for each instance.\n  Use standard shell commands (e.g., adding a `\u0026` at the end of the\n  first docker command) to place docker processes in the\n  background. The 'devel' instance will be available at\n  http://localhost:8787, and the release image at\n  http://localhost:8788\n\n        docker run                                      \\\n            -e PASSWORD=your_password                   \\\n            -p 8787:8787                                \\\n            bioconductor/bioconductor_full:devel\n\n        docker run                                      \\\n            -e PASSWORD=your_password                   \\\n            -p 8788:8787                                \\\n            bioconductor/bioconductor_full:RELEASE_3_10\n\n## Issues in the devel image\n\n### Packages which will never install\n\n1. xps\n\n1. Rmpi\n\n1. ccfindR\n\nFor more information on the issues for this image, please check\n`issues.md`\n\n\n## Singularity\n\nBioconductor provides singularity hub images. The files Singularity, Singularity.RELEASE_3_8, Singularity.RELEASE_3_9 allow the images to build on Singularity hub.\n\nFind the singularity hub images, and download them by https://www.singularity-hub.org/collections/3154/usage\n\n    singularity pull shub://Bioconductor/bioconductor_full\n\n## Frequently Asked Questions (FAQ)\n\n### How do I use LaTeX inside the container?\n\nInstall the `tinytex` package (https://yihui.name/tinytex/) which has helpers for installing LaTeX functionality.\n\n```r\ninstall.packages('tinytex')\ntinytex::install_tinytex()\n```\n\n\n[Bioconductor organization]: https://cloud.docker.com/u/bioconductor/repository/registry-1.docker.io/bioconductor/bioconductor_full\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fbioconductor_full","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioconductor%2Fbioconductor_full","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fbioconductor_full/lists"}