{"id":29224558,"url":"https://github.com/sing-group/pandrugs-docker","last_synced_at":"2025-07-03T06:07:18.159Z","repository":{"id":47409236,"uuid":"125192831","full_name":"sing-group/pandrugs-docker","owner":"sing-group","description":"A Dockerfile to generate an all-in-one pandrugs server","archived":false,"fork":false,"pushed_at":"2024-06-20T14:49:53.000Z","size":2001,"stargazers_count":6,"open_issues_count":2,"forks_count":3,"subscribers_count":8,"default_branch":"master","last_synced_at":"2024-06-21T07:57:16.287Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sing-group.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2018-03-14T10:06:53.000Z","updated_at":"2024-06-20T14:49:57.000Z","dependencies_parsed_at":"2022-09-05T19:51:17.369Z","dependency_job_id":"c78bb0a0-bff5-4e8b-b733-a3de5eeaecda","html_url":"https://github.com/sing-group/pandrugs-docker","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"purl":"pkg:github/sing-group/pandrugs-docker","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fpandrugs-docker","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fpandrugs-docker/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fpandrugs-docker/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fpandrugs-docker/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sing-group","download_url":"https://codeload.github.com/sing-group/pandrugs-docker/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fpandrugs-docker/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263271501,"owners_count":23440396,"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":[],"created_at":"2025-07-03T06:07:17.453Z","updated_at":"2025-07-03T06:07:18.133Z","avatar_url":"https://github.com/sing-group.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# PanDrugs Docker ![release](https://img.shields.io/badge/latest-2024.06-green)\n\nA Dockerfile to generate an all-in-one [PanDrugs](pandrugs.org) server. \n\nLatest version available: `2024.06`\n\n## Requirements\n\nTo be fully functional, in addition to building the `pandrugs2` Docker image as explained below, this PanDrugs server requires:\n\n- An additional Docker image for running VEP. Check [this instructions](vep/README.md) to build and configure the image and see how\n- An additional Docker image for running PharmCat. The official image `pgkb/pharmcat:2.1.2` is used to run [the additional scripts](pandrugs-additional-scripts/README.md).\n\n## Versions of PanDrugs components included in this image\n\n* Front-end: 2.2.0\n* Back-end: 2.3.0\n* Perl variant analysis module: [v20](https://github.com/cnio-bu/pandrugs-db)\n* Database: 20240612\n\nThese versions are packed into the `2024.06` release.\n\n## Versions of databases used by PanDrugs and included this image\n\nThe database sources can be found in the [`pandrugs-db` project](https://github.com/cnio-bu/pandrugs-db).\n\n## Building the image\n\nEdit the `context.xml` file in order to configure the mail system (see [SMTP Configuration Properties](http://connector.sourceforge.net/doc-files/Properties.html) for configuration details).\n\n```\n\u003cResource name=\"mail/session\"\n        auth=\"Container\"\n        type=\"javax.mail.Session\"\n        mail.smtp.host=\"sing.ei.uvigo.es\"\n        mail.smtp.port=\"25\"\n        mail.smtp.auth=\"false\"\n/\u003e\n```\n\nNote that the versions of the PanDrugs components are  are taken from the following environment variables declared in the Dockerfile:\n- `APP_BACKEND_VERSION`\n- `APP_FRONTEND_VERSION`\n- `APP_DB_SCHEMA_VERSION`\n- `APP_DB_DATA_VERSION`\n\nThe available releases for these versions are:\n- `latest` (points to `2024.06`)\n- `2024.06`\n- `2024.05`\n- `2023.03`\n\nThen, inside the cloned repository:\n\n```\ndocker build -t pandrugs2 .\n```\n\nThis process should be relatively fast as database files are downloaded when the server is started for the first time and VEP database files are part of the [pandrugs2-vep](vep/README.md) Docker image. The `pandrugs2` image should be about 1.41GB.\n\n## Starting the server\n\n```\ndocker run -d -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp -v [your_local_dir_for_data OR volume_name]:/pandrugs2-backend_data -p 80:8080 --name pandrugs2 pandrugs2\n```\n\nThis command will:\n- Make your server available via the port `80` at the container machine.\n- Allow the container executing Docker.\n- Share the host `/tmp` directory with the container.\n- Create a Docker managed volume named `pandrugs2-backend_data` if using `-v pandrugs2-backend_data:/pandrugs2-backend_data`\n\nThe first time the container is started, it will download the database files and import them into the MySQL DB. Therefore, this process may take a while and its progress can be monitored with:\n\n```\ndocker logs -f pandrugs2\n```\n\nAs noted in the VEP configuration, create the following symbolic link in the host: `ln -s /var/lib/docker/volumes/pandrugs2-backend_data/_data /pandrugs2-backend_data` (replace `pandrugs2-backend_data` with the actual name of your Docker managed volume). This is because the Docker run commands (created in the `run-pandrugs-vep-*-on-docker.sh` scripts) will use references to directories inside `/pandrugs2-backend_data`. As these commands are executed in the host, such path must exist and point to the actual location of the data (which in this case is the location of the corresponding managed Docker volume).\n\n## Accessing the server\n\nThe frontend will be serving at: http://yourhost\n\nThe backend will be serving at: http://yourhost/pandrugs-backend\n\n## Accessing the database\n\n```\ndocker exec -it pandrugs2 /usr/bin/mysql -uroot\n```\n\n## Getting the pandrugs tomcat log\n\n```\ndocker exec -it pandrugs2 tail -f /pandrugsdb.log\n```\n\n## Stopping the server\n\n```\ndocker stop pandrugs2\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsing-group%2Fpandrugs-docker","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsing-group%2Fpandrugs-docker","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsing-group%2Fpandrugs-docker/lists"}