[{"_1":2,"_189":-5,"_190":-5},"loaderData",{"_3":4,"_17":18,"_25":26,"_167":168},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7,"_13":14,"_15":16},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","theme","system","contrast","normal","routes/_layout",{"_19":-5,"_20":21,"_22":21,"_23":11,"_24":21},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_27":28,"_29":-5,"_30":11,"_31":11,"_32":33,"_34":35,"_36":-5,"_37":11,"_38":39,"_89":90,"_111":112,"_156":-5,"_157":11,"_158":21,"_159":11,"_160":-5,"_161":11,"_162":-5,"_163":164,"_165":113,"_166":-7},"canonicalUrl","https://hub.docker.com/r/systempipe/systempipe_docker/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","systempipe","reponame","systempipe_docker","cloudBuildSource","isAutobuildsAvailable","repo",{"_40":41,"_42":43,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":55,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":64,"_65":66,"_67":-5,"_68":62,"_69":70,"_71":11,"_72":73,"_74":75,"_80":11,"_81":82,"_86":33,"_87":88},"categories",[],"content_types",[44],"image","date_registered","2021-03-09T08:55:05.705962Z","description","","is_private","last_updated","2025-12-03T22:33:03.092036Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[56],"application/vnd.oci.image.index.v1+json","name","pull_count",1652,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","# systemPipeR Docker containers\n\n> Guidelines from [bioconductor_docker](https://github.com/Bioconductor/bioconductor_docker).\n\n# Running the `systemPipeR` with Docker \n\n## Get a copy of the public docker image\n\n````\ndocker pull systempipe/systempipe_docker:latest\n````\n\n## To run RStudio Server:\n\n```\ndocker run -e PASSWORD=systemPipe -p 8787:8787 \\\n systempipe/systempipe_docker:latest\n```\n\nYou can then open a web browser pointing to your docker host on\nport 8787. If you're on Linux and using default settings, the docker\nhost is `127.0.0.1` (or `localhost`, so the full URL to RStudio would\nbe `http://localhost:8787)`. If you are on Mac or Windows and running\n`Docker Toolbox`, you can determine the docker host with the\n`docker-machine ip default` command.\n\nIn the above command, `-e PASSWORD=` is setting the RStudio password\nand is required by the RStudio Docker image. It can be whatever you\nlike except it cannot be `rstudio`. Log in to RStudio with the\nusername `rstudio` and whatever password was specified, in this \nexample `systemPipe`.\n\n## To run R from the command line:\n\n```\ndocker run -it --user rstudio systempipe/systempipe_docker:latest R\n```\n\n## To open a Bash shell on the container:\n\n```\ndocker run -it --user rstudio systempipe/systempipe_docker:latest bash\n```\n\n# Full Documentation\n\nThis tutorial shows how to create, access, run, build a Docker container.\n\n## Table of Content\n\n1. [Install](#Install)\n2. [Docker Hub Account](#dockerHub)\n3. [Log in to the Docker Hub](#login)\n4. [Run Docker](#run)\n5. [Create your first repository](#create)\n6. [Make changes to the container and Create the new image](#changes)\n7. [Commands](#commands)\n8. [Docker and GitHub Actions](#github)\n9. [Common Problems](#faq)\n10. [Singularity Container](#singularity)\n11. [Resources](#resources)\n\n* * *\n

\n\n# Install\n\n**Prerequisites**: \n[Linux](https://docs.docker.com/installation/) \n[Mac](http://docs.docker.com/installation/mac/)\n[Windows](http://docs.docker.com/installation/windows/)\n\nInstructions [here](https://docs.docker.com/engine/install/ubuntu/) on how to install Docker Engine on Ubuntu.\n\n```\nsudo apt-get update\nsudo apt-get install \\\n apt-transport-https \\\n ca-certificates \\\n curl \\\n gnupg\ncurl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg\necho \\\n \"deb [arch=amd64 signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/ubuntu \\\n $(lsb_release -cs) stable\" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null\nsudo apt-get update\nsudo apt-get install docker-ce docker-ce-cli containerd.io\n \n## Verify that Docker Engine is installed correctly by running the hello-world image.\nsudo docker run hello-world\n```\n \n## Uninstall\n\n```\nsudo apt-get remove docker docker-engine docker.io containerd runc\n```\n* * *\n

\n\n# Docker Hub Account\n\nTo be able to share a custom image, please go to https://hub.docker.com and \ncreate a free account.\n\n* * *\n

\n\n## Log in to the Docker Hub locally\n\nLogin with your Docker ID to push and pull images from Docker Hub. If you don't\nhave a Docker ID, head over to https://hub.docker.com to create one.\n\n```\ndocker login\n# Username: XXXX\n# Password: xxx\n# Login Succeeded\n```\n\n* * *\n

\n\n# Run Docker \n\n```\ndocker run-dP systempipe/systempipe_docker:latest\n```\n\nMake sure the container is running:\n```\ndocker ps\n# CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS # NAMES\n#5d007f66a7b3 systempipe/systempipe_docker:latest \"/init\" 5 minutes ago Up 5 minutes 0.0.0.0:49153->8787/tcp determined_easle\n```\n\n## Login to the container\n\nPlease check the `NAMES` in this example, `determined_easle,` to login into the container.\n\n```\ndocker exec -it determined_easle /bin/bash\n```\n\n## Other alternatives to run the container\n\n### To run RStudio Server:\n\n```\ndocker run -e PASSWORD=systemPipe -p 8787:8787 \\\n systempipe/systempipe_docker:latest\n```\n\n### To run R from the command line:\n\n```\ndocker run -it --user rstudio systempipe/systempipe_docker:latest R\n```\n\n### To open a Bash shell on the container:\n\n```\ndocker run -it --user rstudio systempipe/systempipe_docker:latest bash\n```\n\n### Check R Version into the container \n\n```\nR --version\n```\n## Stop Docker\n\n```\ndocker stop determined_easle\n```\n\n* * *\n

\n\n# Create your first repository [Link](https://docs.docker.com/docker-hub/)\n\n## Create a repository:\n\n- Sign in to Docker Hub.\n- Click Create a Repository on the Docker Hub welcome page:\n- Name it /my-repo.\n- Click Create.\n\n## Build and push a container image to Docker Hub from your computer\n\n### Start by creating a *Dockerfile* to specify your application\n\n```\nmkdir docker_test\ncd docker_test\ntouch Dockerfile\n```\n\n```\n# Docker inheritance\nFROM systempipe/systempipe_docker:latest\n\n## Install BiocStyle\nRUN R -e 'BiocManager::install(\"BiocStyle\")'\n\n# Install required Bioconductor package from devel version\nRUN R -e 'BiocManager::install(\"tgirke/systemPipeR\")'\nRUN R -e 'BiocManager::install(\"tgirke/systemPipeRdata\")'\n\nWORKDIR /home/rstudio/SPRojects\n\nCOPY --chown=rstudio:rstudio . /home/rstudio/SPRojects\n\n# Metadata\nLABEL name=\"systempipe/systempipe_docker\" \\\n version=$BIOCONDUCTOR_DOCKER_systempipe \\\n url=\"https://github.com/systemPipeR/systempipe/systempipe_docker\" \\\n vendor=\"systemPipeR Project\" \\\n maintainer=\"email@gmail.com\" \\\n description=\"Bioconductor docker image containing the systemPipeR Project\" \\\n license=\"Artistic-2.0\"\n```\n\n### Run `docker build` to build your Docker image\n\n```\ndocker build -t systempipe/systempipe_docker . \n```\n\n### Run `docker run` to test your Docker image locally\n\n```\ndocker run -e PASSWORD=systemPipe -p 8787:8787 systempipe/systempipe_docker:latest\n```\n\n### Run `docker push` to push your Docker image to Docker Hub\n\n```\ndocker push systempipe/systempipe_docker\n```\n\n- Your repository in Docker Hub should now display a new latest tag under `Tags`\n \n* * *\n

\n\n# Make changes to the container and Create the new image\n\nCreate a folder, for example:\n```\ndocker run -dP systempipe/systempipe_docker\ndocker ps ## To check the NAME \ndocker exec -it lucid_grothendieck /bin/bash\nroot@33c758eb1626:/# R\n```\n\n```r\nsetwd(\"home/rstudio/\")\nsystemPipeRdata::genWorkenvir(\"rnaseq\")\n```\n\n```\nexit\ndocker commit -m \"Added rnaseq template\" -a \"Dani Cassol\" lucid_grothendieck dcassol/systempipeworkshop2021:rnaseq\ndocker push systempipe/systempipe_docker:rnaseq\n```\n\nRun the new image:\n\n```\ndocker run -e PASSWORD=systemPipe -p 8787:8787 systempipe/systempipe_docker:rnaseq\n```\n\n* * *\n

\n\n# Commands\n\n## List which docker machines are available locally\n```docker images```\n\n## List running containers\n```docker ps```\n\n## List all containers\n```docker ps -a```\n\n## Resume a stopped container\n```docker start ```\n\n## Shell into a running container\n```docker exec -it /bin/bash```\n\n## Stop OR remove a cointainer\n```docker stop ```\n```docker rm ```\n\n## Remove a image\n```docker rmi dcassol/systempipeworkshop2021:rnaseq```\n\n* * *\n

\n\n# Docker and GitHub Actions\n\n1. To create a new token, go to Docker Hub Settings\n\n1.1. Account Settings >> Security >> New Access Token\n1.2. Add Access Token Description >> Create\n1.3. Copy the Access Token >> Copy and Close\n\n2. Go to the Repository at GitHub\n\n2.1. Settings > Secrets > New repository secret\n2.2. Create a new secret with the name `DOCKER_HUB_USERNAME` and your `Docker ID` as value\n2.3. Click at Add secret\n2.4. Create a new secret with the name `DOCKER_HUB_ACCESS_TOKEN` and your `Personal Access Token (PAT)` as value (generated in the previous step)\n\n3. Set up the GitHub Actions workflow\n\n```\n steps:\n \n - name: Checkout Repo \n uses: actions/checkout@v2\n\n - name: Login to Docker Hub\n uses: docker/login-action@v1\n with:\n username: ${{ secrets.DOCKER_HUB_USERNAME }}\n password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}\n```\n\n* * *\n

\n\n\n# Common Problems\n\n```\n## Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.24/auth: dial unix /var/run/docker.sock: connect: permission denied\n```\nSolution:\n```{bash, eval=FALSE}\nsudo chmod 666 /var/run/docker.sock\n```\n\n* * *\n

\n\n# Singularity Container\n\nPlease download the Docker image of systemPipe, as follow:\n\n```{bash, eval=FALSE}\nsingularity pull docker://systempipe/systempipe_docker:latest\n```\n\nYou can also use the `build` command to download pre-built images from Docker. \nUnlike `pull`, `build` will convert the image to the latest Singularity image format after \ndownloading it.\n\n```{bash, eval=FALSE}\nsingularity build systempipe_docker_latest.sif docker://systempipe/systempipe_docker:latest\n```\n\nTo run the container:\n\n```{bash, eval=FALSE}\nsingularity shell systempipe_docker_latest.sif\n```\n\n* * *\n

\n\n# Resources\n\n- [Docker Run: How to create images from an application](https://www.mirantis.com/blog/how-do-i-create-a-new-docker-image-for-my-application/)\n- [Docker Hub Quickstart](https://docs.docker.com/docker-hub/)\n- [Configure GitHub Actions](https://docs.docker.com/ci-cd/github-actions/)\n- [Singularity](https://sylabs.io/guides/3.0/user-guide/quick_start.html#interact-with-images)","has_starred","hub_user","dcassol","immutable_tags_settings",{"_76":11,"_77":78},"enabled","rules",[79],".*","is_automated","permissions",{"_83":21,"_84":11,"_85":11},"read","write","admin","user","storage_size",19804546636,"orgData",{"_91":92,"_93":94,"_95":96,"_97":33,"_98":48,"_99":100,"_101":102,"_103":104,"_105":106,"_107":48,"_108":48,"_109":48,"_110":21},"id","c1a462d4c1b64683977f66210d276987","uuid","c1a462d4-c1b6-4683-977f-66210d276987","type","organization","orgname","full_name","location","Riverside/CA","company","systemPipe: Workflow and Visualization Toolkit","profile_url","https://systempipe.org/","date_joined","2021-03-09T05:42:32.5007Z","gravatar_url","gravatar_email","badge","is_active","recentTags",[113],{"_114":44,"_115":116,"_117":118,"_119":120,"_91":121,"_122":123,"_50":145,"_146":116,"_147":73,"_148":56,"_57":149,"_150":151,"_152":130,"_153":145,"_154":66,"_155":21},"content_type","creator",4013415,"digest","sha256:2d89abfef0ba393de92679bbdeefc8a7d801bbf0cf093e83343a1f51da54b84a","full_size",2128879978,140545317,"images",[124,139],{"_125":126,"_117":127,"_128":48,"_129":130,"_131":132,"_133":134,"_135":48,"_136":-5,"_137":120,"_63":66,"_138":-5},"architecture","amd64","sha256:e74a1afa8601e9eabc707ec64386bf0e2ecc1f9b1430b3a7b1e7e89f4404013c","features","last_pulled","2026-09-25T16:38:34.150895195Z","last_pushed","2025-12-03T22:33:00.293039325Z","os","linux","os_features","os_version","size","variant",{"_125":140,"_117":141,"_128":48,"_129":142,"_131":143,"_133":140,"_135":48,"_136":-5,"_137":144,"_63":66,"_138":-5},"unknown","sha256:c8f0befe082fc276b4a051ac4b2b3ddfc399f44a2aa1b09f0aec29c54c4d93e6","2026-09-25T16:38:34.143878433Z","2025-12-03T22:33:01.234895366Z",11120,"2025-12-03T22:33:01.967446Z","last_updater","last_updater_username","media_type","latest","repository",11704445,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"selectedTag","attestationsUrl","routes/_layout.r.$namespace.$reponame.tags",{"_38":169,"_176":177,"_163":187,"_188":11},{"_40":170,"_42":171,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":172,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":64,"_65":66,"_67":-5,"_68":62,"_69":70,"_71":11,"_72":73,"_74":173,"_80":11,"_81":175,"_86":33,"_87":88},[],[44],[56],{"_76":11,"_77":174},[79],{"_83":21,"_84":11,"_85":11},"tags",{"_178":64,"_179":-5,"_180":-5,"_181":182},"count","next","previous","results",[183],{"_114":44,"_115":116,"_117":118,"_119":120,"_91":121,"_122":184,"_50":145,"_146":116,"_147":73,"_148":56,"_57":149,"_150":151,"_152":130,"_153":145,"_154":66,"_155":21},[185,186],{"_125":126,"_117":127,"_128":48,"_129":130,"_131":132,"_133":134,"_135":48,"_136":-5,"_137":120,"_63":66,"_138":-5},{"_125":140,"_117":141,"_128":48,"_129":142,"_131":143,"_133":140,"_135":48,"_136":-5,"_137":144,"_63":66,"_138":-5},[],"canDeleteTags","actionData","errors"]

systempipe/systempipe_docker

Tags for systempipe/systempipe_docker