{"id":40523067,"url":"https://github.com/dockstore/compose_setup","last_synced_at":"2026-01-20T21:13:06.466Z","repository":{"id":37579827,"uuid":"92978674","full_name":"dockstore/compose_setup","owner":"dockstore","description":"Demonstrate how to setup and run Dockstore using composed containers","archived":false,"fork":false,"pushed_at":"2025-09-12T19:50:57.000Z","size":536,"stargazers_count":1,"open_issues_count":0,"forks_count":2,"subscribers_count":5,"default_branch":"develop","last_synced_at":"2025-09-12T22:06:31.379Z","etag":null,"topics":["docker","docker-compose"],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dockstore.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":"SECURITY.md","support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2017-05-31T18:56:20.000Z","updated_at":"2025-08-13T19:44:21.000Z","dependencies_parsed_at":"2023-02-09T16:31:09.872Z","dependency_job_id":"b6b33451-6be2-4eb7-b9a3-576223b3d890","html_url":"https://github.com/dockstore/compose_setup","commit_stats":null,"previous_names":[],"tags_count":46,"template":false,"template_full_name":null,"purl":"pkg:github/dockstore/compose_setup","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dockstore%2Fcompose_setup","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dockstore%2Fcompose_setup/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dockstore%2Fcompose_setup/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dockstore%2Fcompose_setup/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dockstore","download_url":"https://codeload.github.com/dockstore/compose_setup/tar.gz/refs/heads/develop","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dockstore%2Fcompose_setup/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28613894,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-20T18:56:40.769Z","status":"ssl_error","status_checked_at":"2026-01-20T18:54:26.653Z","response_time":117,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["docker","docker-compose"],"created_at":"2026-01-20T21:13:05.777Z","updated_at":"2026-01-20T21:13:06.457Z","avatar_url":"https://github.com/dockstore.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# compose\\_setup\nThis project contains configuration template files needed to run Dockstore using AWS Fargate. View the [dockstore-deploy repository](https://github.com/dockstore/dockstore-deploy)\nfor more information about how Dockstore is setup using AWS Fargate.\nLog issues and see general documentation at [dockstore](https://github.com/ga4gh/dockstore/issues) and [docs.dockstore.org](https://docs.dockstore.org/) respectively\n\nIf you are looking for how to run Dockstore locally as a developer, you are probably in the wrong place and should take a look at https://github.com/dockstore/dockstore/blob/develop/docker-compose.yml\n\n## Prerequisities\n\n1. Tested on Ubuntu 20.04\n1. At least 20GB of disk space, 16GB of RAM, and 4 CPUs\n1. Docker setup following [https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/](https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/) including the post-installation steps for running without sudo\n1. The running Dockstore website will require ports 80 and 443 by default\n1. A client id and client secret for each of the integrations you wish to setup, github and quay.io as a minimum probably. You will need client ids and secrets for each integration as documented on the internal [wiki](https://wiki.oicr.on.ca/display/DOC/OAuth+Apps+and+Other+3rd+Party+Registration).\n\n## Usage\n\n1. Call the install\\_bootstrap script. This templates the contents of `templates` using mustache to the `config` directory while recording your answers for future use.\n\n2. Some additional information on the answers requested in the script\n    1. Each integration requires a client id and a secret, it is worth saying that you should not check these in \n    2. The discourse URL is needed to link Dockstore to a discussion forum \n    3. the Google verification code and tag manager ID are used if you want to properly track visitors to Dockstore and what pages they browse to\n\n3. After following the instructions in the bootstrap script and starting up the site with AWS Fargate, you can browse to the Dockstore site hosted at port 443 by default using `https://\u003cdomain-name\u003e`. \n\nThe current setup relies upon an externally hosted container orchestration service (current AWS ECS with Fargate), externally hosted database (currently AWS RDS) and externally hosted search (currently AWS Elasticsearch). \n    \n### Loading Up a Database ###\n\nLoading up a database is usually not necessary since AWS RDS is persistent. Refer to https://github.com/dockstore/dockstore-deploy#database-setup \n\nNote that database migration is run once during the startup process and is controlled via the `DATABASE_GENERATED` variable. Answer `yes` if you are working as a developer and want to start work from scratch from an empty database. Answer `no` if you are working as an administrator and/or wish to start Dockstore from a production or staging copy of the database.\n\n\n## Logging Usage\n\nIf using with logstash in a container (for development), use `-f docker-compose.yml -f docker-compose.dev.yml` flags after each `docker compose` command to merge docker-compose files (e.g. `docker compose -f docker-compse.yml -f docker-compose.dev.yml build`)\n\nFor example to deploy just logging \n\n```\ndocker compose  -f docker-compose.dev.yml build\nnohup docker compose -f docker-compose.dev.yml up --force-recreate --remove-orphans \u003e/dev/null 2\u003e\u00261 \u0026\ndocker compose -f docker-compose.dev.yml down\ndocker compose -f docker-compose.dev.yml kill\n```\n\n### Kibana Dashboard Setup ###\nImport the [export.json](export.json) Dashboard from compose\\_setup/export.json by going to Kibana's management =\u003e saved objects =\u003e import.  See https://www.elastic.co/guide/en/kibana/current/managing-saved-objects.html for more info, especially the 2nd warning.\n\n## Installing git-secrets\nDockstore uses git-secrets to help make sure that keys and private data stay out\nof the source tree.\nTo install and check for git secrets:\n\n```\nnpm ci\nnpm run install-git secrets\n``` \n\nThis should install git secrets into your local repository and perform a scan. \nIf secrets are found, the run will error and output the potential secret to stdout.\nIf you believe the scan is a false-positive, add the line glob to .gitallowed.\n\n## Handy docker-compose commands:\n    1. `install_bootstrap --script` will template and build everything using your previous answers (useful for quick iteration) \n    2. `docker compose down` will bring all containers down safely\n    3. `nohup docker compose up --force-recreate --remove-orphans \u003e/dev/null 2\u003e\u00261 \u0026` will re-create all containers known to docker-compose and delete those volumes that no longer are associated with running containers\n    4. `docker system prune` for cleaning out old containers and images\n    5. To watch the logs `docker compose logs --follow` while debugging\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdockstore%2Fcompose_setup","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdockstore%2Fcompose_setup","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdockstore%2Fcompose_setup/lists"}