[{"_1":2,"_172":-5,"_173":-5},"loaderData",{"_3":4,"_13":14,"_20":21,"_151":152},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","routes/_layout",{"_15":-5,"_16":17,"_18":17,"_19":11},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","routes/_layout.r.$namespace.$reponame",{"_22":23,"_24":-5,"_25":11,"_26":11,"_27":28,"_29":30,"_31":-5,"_32":11,"_33":34,"_83":84,"_106":107,"_144":-5,"_145":11,"_146":17,"_147":11,"_148":-5,"_149":150},"canonicalUrl","https://hub.docker.com/r/bioconductor/annotationhub_docker/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","bioconductor","reponame","annotationhub_docker","cloudBuildSource","isAutobuildsAvailable","repo",{"_35":36,"_37":38,"_40":41,"_42":43,"_44":11,"_45":46,"_47":48,"_49":50,"_52":30,"_27":28,"_53":54,"_55":39,"_56":57,"_58":59,"_60":61,"_62":-5,"_63":57,"_64":65,"_66":11,"_67":28,"_68":69,"_74":17,"_75":76,"_80":28,"_81":82},"categories",[],"content_types",[39],"image","date_registered","2016-01-25T18:55:03.639403Z","description","Annotation Hub","is_private","last_updated","2020-03-03T16:29:24.101414Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[51],"application/vnd.docker.container.image.v1+json","name","pull_count",885,"repository_type","star_count",0,"status",1,"status_description","active","source","collaborator_count","full_description","\n# Docker Container for AnnotationHub Server\n\n## Important Note\n\nThe way this Docker Container is currently set up,\nit can only be used by Bioconductor core members\nwho have access to the production server\nand know its credentials.\n\nIt should probably change so it can be used by\nanyone who wants to test recipes. But that\nis not going to happen right away.\n\n## Table of Contents\n\n- [Setting up the docker container](#setup)\n\t- [Prerequisites](#prerequisites)\n - [Run the continer](#run)\n\t- [Determine URL of server](#url)\n- [Using the container](#use)\n- [Testing the changes](#test)\n- [Pushing changes to production](#push)\n\n\n## Setting up the docker container\n\n\n### Prerequisites\n\nSet the environment variable `MYSQL_REMOTE_PASSWORD` to\nthe correct value, found in the \"AnnotationHub production\nserver\" section of the Google Doc \"Credentials For\nBioconductor Cloud resources\".\n\nThe container will not work properly unless this is set.\n\nYou can set it by doing:\n\n export MYSQL_REMOTE_PASSWORD=XXX\n\nwhere XXX is replaced with the correct password. This password should also be \nadded to 'MYSQL_REMOTE_PASSWORD:' in the docker-compose.yml file.\n\nIf you are on Linux, install docker using\n[Docker Engine](https://docs.docker.com/installation/). Also install\n[Docker Compose](https://docs.docker.com/compose/install/).\nIf you are on Mac or Windows, install Docker Desktop instead. You will not need \nto install Docker Compose because it is included in Docker Desktop.\n[Docker Desktop for Mac](https://docs.docker.com/docker-for-mac/install/),\n[Docker Desktop for Windows](https://docs.docker.com/docker-for-windows/install/).\n\nClone the AnnotationHubServer3.0 code to the same directory as \nthis README:\n\n git clone https://github.com/Bioconductor/AnnotationHubServer3.0.git\n\nOr if you already have this repository checked out elsewhere\non your system, make a symbolic link to it in the current directory\n(the same directory as this README).\n\nCreate a directory called \"data\" in the same directory as\nthis README.\n\n\n### Run The Container\n\nOpen a terminal window (a Docker Quickstart Terminal if\nyou are on Mac or windows) and change to the same\ndirectory where this README is. Issue the command:\n\n docker-compose up\n\nThis command will *pull down the database contents\nfrom the production AnnotationHub server* and then\nstart a local server.\n\nWhen you see a line like this:\n\n annotationhub_1 | == Shotgun/WEBrick on http://0.0.0.0:3000/\n\n...the AnnotationHub server is running in the container.\n\nTo verify that it is running, you can determine its URL\n(in the next section).\n\n\n### Determining URL of server\n\nIf you are on linux, the URL of the server is likely\n[http://localhost:3000/resource](http://localhost:3000/resource).\n\nIf you are in the cloud you need to use the public DNS name of your instance\nas your IP address.\n\nIf you are using boot2docker (deprecated by Docker Toolbox),\nyou can determine your Docker host's IP address with the command\n`boot2docker ip`. If this returns `1.2.3.4`, your URL\nwould be `http://1.2.3.4:3000/resource`. \n\nIf you are using Docker Toolbox, the command to determine\nyour Docker host's IP address is \n\n docker-machine ip default\n\nIf this returns `1.2.3.4`, your URL would be\n`http://1.2.3.4:3000/resource`.\n\n\n## Using the container\n\nStart a new R session in a new terminal window. \nAssuming your server URL \nis `http://1.2.3.4:3000/resource`, enter the following\nat the R prompt:\n\n options(AH_SERVER_POST_URL=\"http://1.2.3.4:3000/resource\") ## used by AnnotationHubData to insert metadata\n options(ANNOTATION_HUB_URL=\"http://1.2.3.4:3000\") ## used by AnnotationHub to get metadata\n\nReplace the URL with your actual URL, of course. These options must be set before loading `AnnotationHub` and `AnnotationHubData`.\n\n\tlibrary(AnnotationHub)\n\tlibrary(AnnotationHubData)\n\nNow you can run recipes, etc. and the insertions will\nhappen inside the docker container, not in the production\ndatabase.\n\n\n## Testing the changes\n\nYou can interact with the docker db with R or mysql.\n\n#### R session\n\nTo view the docker db from R you must first convert the mysql db to sqlite. From another terminal window do\n\n\tdocker exec -ti annotationhub_annotationhub_1 bash\n\nThat will log you in to the annotationhub server container. Then do the following:\n\n\tcd /AnnotationHubServer3.0/\n\truby convert_db.rb \n\nThat will convert the mysql database to sqlite. You can then type\n\n\texit\n\t\nto exit the container, start R and set the variables as described in [Using the container](#use). AnnotationHub should recognize that there are changes and download the new sqlite database, but if not you can remove the old one from your cache to trigger a copy.\n\n#### mysql session\n\nmysql is not exposed to the host, so you need to do this from the mysql machine. Run\n\n\tdocker ps\n\t\nto see a list of containers that are running. One will have the string 'db' in it. Let's say the full name is 'db1'. Connect to the container with:\n\n\tdocker exec -ti db_1 bash\n\nFrom within the resulting prompt start mysql and query the db as usual:\n\n\tmysql -p -u ahuser\n\t\nWhen you are satisfied that the changes you have made are \ncorrect, you can update the production database (see next\nsection). If you have messed up and you don't want to\npush your changes to production, you can just exit\nthe container (press Control-C in the window where it is\nrunning) and start over again.\n\n\n## Pushing changes to production\n\nYou need to back up the database inside the docker \ncontainer. You can do it like this:\n\n docker exec annotationhub_annotationhub_1 bash /bin/backup_db.sh\n\nNote that `annotationhub_annotationhub_1` is the name of the\ndocker container that has the annotation hub server on it; this\nname may vary, the `docker ps` command will give you the\naccurate container name.\n\nNow in the `data` directory on your local machine, \nthere is a file called `annotationhub.sql.gz`. Upload this to the production machine.\n\nLog into the production machine and make a backup of production db:\n\n mysqldump -p -u ahuser annotationhub | gzip > dbdump_YYYY_MM_DD_fromProd.sql.gz\n\nDrop the old db and create an empty one:\n\n mysql -p -u root\n drop database annotationhub;\n create database annotationhub;\n quit;\n\nFill the empty with the modified db:\n\n zcat dbdump_YYYY_MM_DD_fromDocker.sql.gz | mysql -p -u root annotationhub\n","has_starred","hub_user","immutable_tags_settings",{"_70":11,"_71":72},"enabled","rules",[73],".*","is_automated","permissions",{"_77":17,"_78":11,"_79":11},"read","write","admin","user","storage_size",1933864387,"orgData",{"_85":86,"_87":88,"_89":90,"_91":28,"_92":93,"_94":95,"_96":97,"_98":99,"_100":101,"_102":93,"_103":93,"_104":93,"_105":17},"id","2c5bb01674c011e4bea40242ac11001b","uuid","2c5bb016-74c0-11e4-bea4-0242ac11001b","type","organization","orgname","full_name","","location","Boston, MA, USA","company","Bioconductor","profile_url","http://bioconductor.org/","date_joined","2014-11-19T21:44:32.734936Z","gravatar_url","gravatar_email","badge","is_active","recentTags",[108],{"_109":39,"_110":111,"_112":113,"_85":114,"_115":116,"_45":133,"_134":111,"_135":28,"_136":51,"_52":137,"_138":139,"_140":124,"_141":133,"_142":61,"_143":17},"content_type","creator",150968,"full_size",276268368,85629569,"images",[117],{"_118":119,"_120":121,"_122":93,"_123":124,"_125":126,"_127":128,"_129":93,"_130":-5,"_131":113,"_58":61,"_132":-5},"architecture","amd64","digest","sha256:16aff90f4d242c948e16261f86c5084b0212c3842d6cf0b9123d54983eb30051","features","last_pulled","2026-09-10T14:15:33.449783092Z","last_pushed","2020-03-03T16:29:24Z","os","linux","os_features","os_version","size","variant","2020-03-03T16:29:23.755515Z","last_updater","last_updater_username","media_type","latest","repository",497227,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"routes/_layout.r.$namespace.$reponame.tags",{"_33":153,"_160":161,"_149":170,"_171":11},{"_35":154,"_37":155,"_40":41,"_42":43,"_44":11,"_45":46,"_47":48,"_49":156,"_52":30,"_27":28,"_53":54,"_55":39,"_56":57,"_58":59,"_60":61,"_62":-5,"_63":57,"_64":65,"_66":11,"_67":28,"_68":157,"_74":17,"_75":159,"_80":28,"_81":82},[],[39],[51],{"_70":11,"_71":158},[73],{"_77":17,"_78":11,"_79":11},"tags",{"_162":59,"_163":-5,"_164":-5,"_165":166},"count","next","previous","results",[167],{"_109":39,"_110":111,"_112":113,"_85":114,"_115":168,"_45":133,"_134":111,"_135":28,"_136":51,"_52":137,"_138":139,"_140":124,"_141":133,"_142":61,"_143":17},[169],{"_118":119,"_120":121,"_122":93,"_123":124,"_125":126,"_127":128,"_129":93,"_130":-5,"_131":113,"_58":61,"_132":-5},[],"canDeleteTags","actionData","errors"]

bioconductor/annotationhub_docker

Tags for bioconductor/annotationhub_docker