{"id":19592803,"url":"https://github.com/soedinglab/mmseqs2-app","last_synced_at":"2025-04-06T17:11:23.049Z","repository":{"id":39998438,"uuid":"130207742","full_name":"soedinglab/MMseqs2-App","owner":"soedinglab","description":"MMseqs2 app to run on your workstation or servers","archived":false,"fork":false,"pushed_at":"2025-03-24T06:19:17.000Z","size":11317,"stargazers_count":75,"open_issues_count":20,"forks_count":24,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-03-30T16:11:54.077Z","etag":null,"topics":["alphafold2","bioinformatics","colabfold","docker","docker-compose","electron","foldseek","golang","mmseqs","profile-search","sequence-search","structure-search","vue"],"latest_commit_sha":null,"homepage":"https://search.foldseek.com","language":"Vue","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/soedinglab.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}},"created_at":"2018-04-19T11:49:04.000Z","updated_at":"2025-03-28T12:21:45.000Z","dependencies_parsed_at":"2023-09-27T19:38:55.976Z","dependency_job_id":"fbd6657a-777e-46e5-801b-2732a0864907","html_url":"https://github.com/soedinglab/MMseqs2-App","commit_stats":null,"previous_names":[],"tags_count":9,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2FMMseqs2-App","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2FMMseqs2-App/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2FMMseqs2-App/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2FMMseqs2-App/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/soedinglab","download_url":"https://codeload.github.com/soedinglab/MMseqs2-App/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247517912,"owners_count":20951718,"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":["alphafold2","bioinformatics","colabfold","docker","docker-compose","electron","foldseek","golang","mmseqs","profile-search","sequence-search","structure-search","vue"],"created_at":"2024-11-11T08:37:03.643Z","updated_at":"2025-04-06T17:11:23.011Z","avatar_url":"https://github.com/soedinglab.png","language":"Vue","readme":"# App and Server for MMseqs2, Foldseek, FoldMason and ColabFold\n[MMseqs2](https://github.com/soedinglab/MMseqs2) and [Foldseek](https://github.com/steineggerlab/foldseek) are software suites to search and annotate huge sequence and structure sets. We built a graphical interface for interactive data exploration. Check out a live instance for [MMseqs2](https://search.mmseqs.com) and for [Foldseek/FoldMason](https://search.foldseek.com). Additionally, this codebase holds the API server for [ColabFold](https://github.com/sokrypton/ColabFold).\n\nThe application runs either:\n* on your server through docker-compose, where it can make your sequence, profile or structure databases easily accessible over the web\n* on your workstation as a cross-platform desktop application with the help of [Electron](https://github.com/electron/electron)\n\n\u003cp align=\"center\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/soedinglab/mmseqs2-app/master/.github/stickers.png\" height=\"384\" /\u003e\u003c/p\u003e\n\n## Desktop App\nHead over to the [release page](https://github.com/soedinglab/MMseqs2-App/releases) and download the latest version. We support Linux, macOS and Windows.\n\n\u003e [!IMPORTANT]\n\u003e The desktop app is currently not maintained. Currently, only the backend-only mode for ColabFold and the MMseqs2 and Foldseek webservers are being maintained. We will revisit the desktop app at some point in the future.\n\n### Adding a search database\nOnce the app is installed, open the Settings panel. There you can add either sequence databases in FASTA format, such as our [Uniclust](https://uniclust.mmseqs.com/) databases or profile databases in Stockholm format, such as the [PFAM](ftp://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz).\n\n## Web app quick start with docker-compose\nMake sure you have `docker`, `docker-compose` and `git` installed on your server.\nTo start the MMseqs2/Foldseek web server execute the following commands. Afterwards you can navigate to http://localhost:8877 to access the interface.\n\n``` bash\n# clone the repository\ngit clone https://github.com/soedinglab/MMseqs2-App.git\n\n# navigate to our docker recipes\ncd MMseqs2-App/docker-compose\n\n# (optional) edit the APP entry in the .env file to choose between mmseqs and foldseek\n\n# list available databases\ndocker-compose run db-setup\n\n# download PDB\ndocker-compose run db-setup PDB\n\n# start the server with docker-compose\ndocker-compose up\n```\n\nBy default, the server will start on port 8877. You can edit the `.env` file in the `docker-compose` directory to change this port.\n\nHead over to the [docker-compose readme](https://github.com/soedinglab/MMseqs2-App/blob/master/docker-compose/README.md) for more details on running your own server, including how to add your own sequence, profile or structure databases. Take a look at the [API documentation](https://search.mmseqs.com/docs) to learn how to talk to the server backend.\n\n## Building the desktop app\n\nYou need to have `git`, `go` (\u003e=1.18), `node`, `npm` and `make` installed on your system.\n\nAfterwards run the following commands, and the apps will appear in the `build` folder.\n\n``` bash\n# clone the repository\ngit clone https://github.com/soedinglab/MMseqs2-App.git\ncd MMseqs2-App\n\n# install all dependencies\nnpm install\n\n# build the app for all platforms, choose either mmseqs or foldseek\nFRONTEND_APP=mmseqs npm run electron:build\n```\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsoedinglab%2Fmmseqs2-app","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsoedinglab%2Fmmseqs2-app","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsoedinglab%2Fmmseqs2-app/lists"}