{"id":21274791,"url":"https://github.com/maayanlab/rummagene","last_synced_at":"2025-07-11T06:34:37.268Z","repository":{"id":209500089,"uuid":"674826023","full_name":"MaayanLab/rummagene","owner":"MaayanLab","description":null,"archived":false,"fork":false,"pushed_at":"2025-06-03T21:53:28.000Z","size":63467,"stargazers_count":11,"open_issues_count":7,"forks_count":3,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-06-04T02:12:34.842Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://rummagene.com","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MaayanLab.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-08-04T22:17:20.000Z","updated_at":"2025-06-03T21:53:26.000Z","dependencies_parsed_at":"2024-02-08T19:24:30.090Z","dependency_job_id":"3e389638-d7db-4e4c-a163-1a136f21950d","html_url":"https://github.com/MaayanLab/rummagene","commit_stats":null,"previous_names":["maayanlab/rummagene"],"tags_count":25,"template":false,"template_full_name":null,"purl":"pkg:github/MaayanLab/rummagene","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Frummagene","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Frummagene/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Frummagene/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Frummagene/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MaayanLab","download_url":"https://codeload.github.com/MaayanLab/rummagene/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Frummagene/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":264748736,"owners_count":23658059,"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":"2024-11-21T09:25:37.120Z","updated_at":"2025-07-11T06:34:36.272Z","avatar_url":"https://github.com/MaayanLab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Rummagene\n\n\u003chttps://rummagene.com/\u003e\n\nThis is a webserver for gene set enrichment analysis on a very large gene set -- one constructed by extracting gene sets from PMC OA. The [bot](https://github.com/MaayanLab/rummagene/tree/main/bot) does the extraction weekly.\n\n## Development\nRather than splitting up the meta and data APIs, all functionality is incorporated into a postgres database.\n\nWe use postgraphile to serve the database on a graphql endpoint -- this endpoint can then be used for all necessary functionality, including both metadata search, filtering, and enrichment analysis. For speed purposes, enrichment is done through a companion API written in rust, the database itself communicates with this API, it is transparent to the application or users of the database.\n\n### Usage\n```bash\n# prepare environment variables\ncp .env.example .env\n# review \u0026 edit .env\n\n# start db\ndocker-compose up -d postgres\n\n# create db/ensure it's fully migrated\ndbmate up\n\n# start companion API\ndocker-compose up -d enrich\n\n# start app (production)\ndocker-compose up -d app\n# start app (development)\nnpm run dev\n```\n\n### Provisioning\n```bash\nPYTHONPATH=bot python -m helper ingest -i your-gmt.gmt\nPYTHONPATH=bot python -m helper ingest-paper-info\nPYTHONPATH=bot python -m helper ingest-gene-info\n```\n\n### Writing Queries\nSee `src/graphql/core.graphql`\nThese can be tested/developed at \u003chttp://localhost:3000/graphiql\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaayanlab%2Frummagene","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmaayanlab%2Frummagene","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaayanlab%2Frummagene/lists"}