{"id":19624238,"url":"https://github.com/bioconductor/bioc_docker","last_synced_at":"2025-06-27T22:06:38.583Z","repository":{"id":24945832,"uuid":"28363453","full_name":"Bioconductor/bioc_docker","owner":"Bioconductor","description":"[DEPRECATED] Docker containers for Bioconductor","archived":false,"fork":false,"pushed_at":"2023-03-15T20:25:37.000Z","size":4197,"stargazers_count":49,"open_issues_count":6,"forks_count":26,"subscribers_count":19,"default_branch":"devel","last_synced_at":"2025-04-28T05:35:05.184Z","etag":null,"topics":["bioconductor-dockers"],"latest_commit_sha":null,"homepage":"https://github.com/bioconductor/bioconductor_docker","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"artistic-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":"2014-12-22T22:44:51.000Z","updated_at":"2023-03-15T20:25:41.000Z","dependencies_parsed_at":"2023-10-20T18:25:41.821Z","dependency_job_id":null,"html_url":"https://github.com/Bioconductor/bioc_docker","commit_stats":null,"previous_names":[],"tags_count":157,"template":false,"template_full_name":null,"purl":"pkg:github/Bioconductor/bioc_docker","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fbioc_docker","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fbioc_docker/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fbioc_docker/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fbioc_docker/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Bioconductor","download_url":"https://codeload.github.com/Bioconductor/bioc_docker/tar.gz/refs/heads/devel","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Bioconductor%2Fbioc_docker/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":262341617,"owners_count":23296069,"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-dockers"],"created_at":"2024-11-11T11:37:22.727Z","updated_at":"2025-06-27T22:06:38.556Z","avatar_url":"https://github.com/Bioconductor.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# Bioconductor Dockers - DEPRECATED #\n\n## Deprecation Notice\n\nThese set of images and code have been DEPRECATED in favor of\nhttps://github.com/Bioconductor/bioconductor_docker. \n\nWe will support the containers till Release 3.11, i.e the current\nrelease 3.10 will be the last maintained release.\n\n## Overview ##\n\nThis repository contains Dockerfiles for different Docker containers of interest\nfor Bioconductor users.  Additional information about available containers,\ninstallation and modification can be found on the [Bioconductor Docker\nPage](http://bioconductor.org/help/docker/) or [Docker\ninstallation](https://docs.docker.com/installation/).\n\n\n## Available Docker Containers ##\n\nSee also [Bioconductor Docker Page](http://bioconductor.org/help/docker/).\n\n#### Maintained by the Bioconductor Core Team: bioc-issue-bot@bioconductor.org:\n\n| Docker Container  | Docker Hub Latest Version  | Image Size | Build status\n| :------------------------- | :----------------- | :---------- | :----------\n| release_base2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/release_base)) ([DockerHub](https://hub.docker.com/r/bioconductor/release_base2/)) | [![](https://images.microbadger.com/badges/version/bioconductor/release_base2:R3.6.1_Bioc3.9.svg)](https://hub.docker.com/r/bioconductor/release_base2/)  | [![](https://images.microbadger.com/badges/image/bioconductor/release_base2:R3.6.1_Bioc3.9.svg)](https://hub.docker.com/r/bioconductor/release_base2/)| [![](https://img.shields.io/docker/cloud/build/bioconductor/release_base2.svg)](https://hub.docker.com/r/bioconductor/release_base2/builds/)\n| release_core2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/release_core)) ([DockerHub](https://hub.docker.com/r/bioconductor/release_core2/)) | [![](https://images.microbadger.com/badges/version/bioconductor/release_core2:R3.6.1_Bioc3.9.svg)](https://hub.docker.com/r/bioconductor/release_core2/)  | [![](https://images.microbadger.com/badges/image/bioconductor/release_core2:R3.6.1_Bioc3.9.svg)](https://hub.docker.com/r/bioconductor/release_core2/) | [![](https://img.shields.io/docker/cloud/build/bioconductor/release_core2.svg)](https://hub.docker.com/r/bioconductor/release_core2/builds/)\n| devel_base2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/devel_base)) ([DockerHub](https://hub.docker.com/r/bioconductor/devel_base2/)) | [![](https://images.microbadger.com/badges/version/bioconductor/devel_base2.svg)](https://hub.docker.com/r/bioconductor/devel_base2/) | [![](https://images.microbadger.com/badges/image/bioconductor/devel_base2.svg)](https://hub.docker.com/r/bioconductor/devel_base2/) | [![](https://img.shields.io/docker/cloud/build/bioconductor/devel_base2.svg)](https://hub.docker.com/r/bioconductor/devel_base2/builds/)\n| devel_core2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/devel_core)) ([DockerHub](https://hub.docker.com/r/bioconductor/devel_core2/)) | [![](https://images.microbadger.com/badges/version/bioconductor/devel_core2.svg)](https://hub.docker.com/r/bioconductor/devel_core2/)  | [![](https://images.microbadger.com/badges/image/bioconductor/devel_core2.svg)](https://hub.docker.com/r/bioconductor/devel_core2/) | [![](https://img.shields.io/docker/cloud/build/bioconductor/devel_core2.svg)](https://hub.docker.com/r/bioconductor/devel_core2/builds/)\n\n\n#### Maintained by Steffen Neumann: sneumann@ipb-halle.de\nMaintained as part of the “PhenoMeNal, funded by Horizon2020 grant 654241”\n\n| Docker Container  | Docker Hub Latest Version  | Image Size | Build status\n| :------------------------- | :----------------- | :---------- | :----------\n| release_protmetcore2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/release_protmetcore)) ([DockerHub](https://hub.docker.com/r/bioconductor/release_protmetcore2/)) | [![](https://images.microbadger.com/badges/version/bioconductor/release_protmetcore2:R3.6.1_Bioc3.9.svg)](https://hub.docker.com/r/bioconductor/release_protmetcore2/) | [![](https://images.microbadger.com/badges/image/bioconductor/release_protmetcore2:R3.6.1_Bioc3.9.svg)](https://hub.docker.com/r/bioconductor/release_protmetcore2/)  | [![](https://img.shields.io/docker/cloud/build/bioconductor/release_protmetcore2.svg)](https://hub.docker.com/r/bioconductor/release_protmetcore2/builds/)\n| release_metabolomics2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/release_metabolomics)) ([DockerHub](https://hub.docker.com/r/bioconductor/release_metabolomics2/)) | [![](https://images.microbadger.com/badges/version/bioconductor/release_metabolomics2:R3.6.1_Bioc3.9.svg)](https://hub.docker.com/r/bioconductor/release_metabolomics2/) | [![](https://images.microbadger.com/badges/image/bioconductor/release_metabolomics2:R3.6.1_Bioc3.9.svg)](https://hub.docker.com/r/bioconductor/release_metabolomics2/) | [![](https://img.shields.io/docker/cloud/build/bioconductor/release_metabolomics2.svg)](https://hub.docker.com/r/bioconductor/release_metabolomics2/builds/)\n| devel_protmetcore2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/devel_protmetcore)) ([DockerHub](https://hub.docker.com/r/bioconductor/devel_protmetcore2/)) | [![](https://images.microbadger.com/badges/version/bioconductor/devel_protmetcore2.svg)](https://hub.docker.com/r/bioconductor/devel_protmetcore2/) | [![](https://images.microbadger.com/badges/image/bioconductor/devel_protmetcore2.svg)](https://hub.docker.com/r/bioconductor/devel_protmetcore2/) | [![](https://img.shields.io/docker/cloud/build/bioconductor/devel_protmetcore2.svg)](https://hub.docker.com/r/bioconductor/devel_protmetcore2/builds/)\n| devel_metabolomics2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/devel_metabolomics)) ([DockerHub](https://hub.docker.com/r/bioconductor/devel_metabolomics2/)) | [![](https://images.microbadger.com/badges/version/bioconductor/devel_metabolomics2.svg)](https://hub.docker.com/r/bioconductor/devel_metabolomics2/) | [![](https://images.microbadger.com/badges/image/bioconductor/devel_metabolomics2.svg)](https://hub.docker.com/r/bioconductor/devel_metabolomics2/) | [![](https://img.shields.io/docker/cloud/build/bioconductor/devel_metabolomics2.svg)](https://hub.docker.com/r/bioconductor/devel_metabolomics2/builds/)\n\n\n#### Maintained by Laurent Gatto: lg390@cam.ac.uk\n\n| Docker Container  | Docker Hub Latest Version  | Image Size | Build status\n| :------------------------- | :----------------- | :---------- | :----------\n| release_mscore2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/release_mscore)) ([DockerHub](https://hub.docker.com/r/bioconductor/release_mscore2/)) | [![](https://images.microbadger.com/badges/version/bioconductor/release_mscore2:R3.6.1_Bioc3.9.svg)](https://hub.docker.com/r/bioconductor/release_mscore2/) | [![](https://images.microbadger.com/badges/image/bioconductor/release_mscore2:R3.6.1_Bioc3.9.svg)](https://hub.docker.com/r/bioconductor/release_mscore2/)  | [![](https://img.shields.io/docker/cloud/build/bioconductor/release_mscore2.svg)](https://hub.docker.com/r/bioconductor/release_mscore2/builds/)\n| release_protcore2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/release_protcore)) ([DockerHub](https://hub.docker.com/r/bioconductor/release_protcore2/)) | [![](https://images.microbadger.com/badges/version/bioconductor/release_protcore2:R3.6.1_Bioc3.9.svg)](https://hub.docker.com/r/bioconductor/release_protcore2/) | [![](https://images.microbadger.com/badges/image/bioconductor/release_protcore2:R3.6.1_Bioc3.9.svg)](https://hub.docker.com/r/bioconductor/release_protcore2/) | [![](https://img.shields.io/docker/cloud/build/bioconductor/release_protcore2.svg)](https://hub.docker.com/r/bioconductor/release_protcore2/builds/)\n| release_proteomics2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/release_proteomics)) ([DockerHub](https://hub.docker.com/r/bioconductor/release_proteomics2/)) | [![](https://images.microbadger.com/badges/version/bioconductor/release_proteomics2:R3.4.4_Bioc3.6.svg)](https://hub.docker.com/r/bioconductor/release_proteomics2/) | [![](https://images.microbadger.com/badges/image/bioconductor/release_proteomics2:R3.4.4_Bioc3.6.svg)](https://hub.docker.com/r/bioconductor/release_proteomics2/) | [![](https://img.shields.io/docker/cloud/build/bioconductor/release_proteomics2.svg)](https://hub.docker.com/r/bioconductor/release_proteomics2/builds/)\n| devel_mscore2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/devel_mscore)) ([DockerHub](https://hub.docker.com/r/bioconductor/devel_mscore2/)) | [![](https://images.microbadger.com/badges/version/bioconductor/devel_mscore2.svg)](https://hub.docker.com/r/bioconductor/devel_mscore2/) | [![](https://images.microbadger.com/badges/image/bioconductor/devel_mscore2.svg)](https://hub.docker.com/r/bioconductor/devel_mscore2/) | [![](https://img.shields.io/docker/cloud/build/bioconductor/devel_mscore2.svg)](https://hub.docker.com/r/bioconductor/devel_mscore2/builds/)\n| devel_protcore2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/devel_protcore)) ([DockerHub](https://hub.docker.com/r/bioconductor/devel_protcore2/)) | [![](https://images.microbadger.com/badges/version/bioconductor/devel_protcore2.svg)](https://hub.docker.com/r/bioconductor/devel_protcore2/) | [![](https://images.microbadger.com/badges/image/bioconductor/devel_protcore2.svg)](https://hub.docker.com/r/bioconductor/devel_protcore2/) | [![](https://img.shields.io/docker/cloud/build/bioconductor/devel_protcore2.svg)](https://hub.docker.com/r/bioconductor/devel_protcore2/builds/)\n| devel_proteomics2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/devel_proteomics)) ([DockerHub](https://hub.docker.com/r/bioconductor/devel_proteomics2/)) | [![](https://images.microbadger.com/badges/version/bioconductor/devel_proteomics2.svg)](https://hub.docker.com/r/bioconductor/devel_proteomics2/) | [![](https://images.microbadger.com/badges/image/bioconductor/devel_proteomics2.svg)](https://hub.docker.com/r/bioconductor/devel_proteomics2/) | [![](https://img.shields.io/docker/cloud/build/bioconductor/devel_proteomics2.svg)](https://hub.docker.com/r/bioconductor/devel_proteomics2/builds/)\n\n#### Maintained by RGLab: wjiang2@fredhutch.org\n\n| Docker Container  | Docker Hub Latest Version  | Image Size | Build status\n| :------------------------- | :----------------- | :---------- | :----------\n| release_cytometry2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/release_cytometry)) ([DockerHub](https://hub.docker.com/r/bioconductor/release_cytometry2/)) | [![](https://images.microbadger.com/badges/version/bioconductor/release_cytometry2:R3.6.1_Bioc3.9.svg)](https://hub.docker.com/r/bioconductor/release_cytometry2/) | [![](https://images.microbadger.com/badges/image/bioconductor/release_cytometry2:R3.6.1_Bioc3.9.svg)](https://hub.docker.com/r/bioconductor/release_cytometry2/) | [![](https://img.shields.io/docker/cloud/build/bioconductor/release_cytometry2.svg)](https://hub.docker.com/r/bioconductor/release_cytometry2/builds/)\n| devel_cytometry2 ([GitHub](https://github.com/Bioconductor/bioc_docker/tree/master/out/devel_cytometry)) ([DockerHub](https://hub.docker.com/r/bioconductor/devel_cytometry2/)) | [![](https://images.microbadger.com/badges/version/bioconductor/devel_cytometry2.svg)](https://hub.docker.com/r/bioconductor/devel_cytometry2/) | [![](https://images.microbadger.com/badges/image/bioconductor/devel_cytometry2.svg)](https://hub.docker.com/r/bioconductor/devel_cytometry2/) | [![](https://img.shields.io/docker/cloud/build/bioconductor/devel_cytometry2.svg)](https://hub.docker.com/r/bioconductor/devel_cytometry2/builds/)\n\n### General Docker Usage\n\nA well organized guide to popular docker commands can be found\n[here](https://github.com/wsargent/docker-cheat-sheet). For convenience, below\nare some commands to get you started.\n**Note:** You may need to add sudo before each command\n\n##### List which docker machines are available locally\n    docker images\n##### List running containers\n    docker ps\n##### List all containers\n    docker ps -a\n##### Get container IP address\n    docker inspect --format '{{ .NetworkSettings.IPAddress }}' \u003cname\u003e\n##### Get a copy of public docker\n    docker pull \u003cname\u003e\n##### Keep a container running at startup\n    docker run -itd \u003cname\u003e\n##### Shutdown container\n    docker stop \u003cname\u003e\n##### Resume container\n    docker start \u003cname\u003e\n\n##### Delete container\n    docker rm \u003cname\u003e\n##### Shell into a running container with either of the following:\n    docker exec -it \u003cname\u003e /bin/bash\n    docker attach \u003cname\u003e\n\n##### Mount a volume\n\nIt is possible to mount/map an additional volume or directory. This might be\nuseful for say mounting a local R install directory for use on the docker. The\npath on the docker image that should be mapped to the additional volume is\n`/usr/local/lib/R/host-site-library`.  The follow example would mount my locally\ninstalled packages to this docker directory. In turn, that path is automatically\nloaded in the R `.libPaths` on the docker image and all of my locally installed\npackage would be available for use.\n\n    sudo docker run -v /home/lori/R/x86_64-pc-linux-gnu-library/3.5-BioC-3.8:/usr/local/lib/R/host-site-library -it \u003cname\u003e  \n\n##### User account\n\nIf running command line rather than with rstudio, please use the bioc user\naccount\n\n    sudo docker run -ti --user bioc \u003cname\u003e R\n\n##### Building and modifying the Bioconductor docker images\n\nThe BioC Dockerfiles are not directly edited. Instead,\nfor each biocView, there is a common `Dockerfile.in`,\nfrom which two output files for `release` and `devel` files are generated by running\nthe `rake` command. All the creation is controlled by the `Rakefile`,\nwhich will also take care if any of the dependencies (i.e. the *.in files) have changed.\n\nE.g. the `Dockerfile` for the BioC development branch for core packages\nis created from `src/core/Dockerfile.in` and placed into\n`out/devel_core/Dockerfile`.\n\n\n##### More Help\n\nPlease also see https://bioconductor.org/help/docker/\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fbioc_docker","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbioconductor%2Fbioc_docker","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbioconductor%2Fbioc_docker/lists"}