{"id":18480607,"url":"https://github.com/fjossinet/assemble2docker","last_synced_at":"2026-01-24T19:52:07.269Z","repository":{"id":77695556,"uuid":"55237339","full_name":"fjossinet/Assemble2Docker","owner":"fjossinet","description":"A docker image containing the RNA algorithms needed by Assemble2","archived":false,"fork":false,"pushed_at":"2017-03-16T09:28:07.000Z","size":7,"stargazers_count":3,"open_issues_count":1,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-05-13T19:24:35.180Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/fjossinet.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":"2016-04-01T14:13:33.000Z","updated_at":"2024-03-14T17:05:46.000Z","dependencies_parsed_at":null,"dependency_job_id":"d1f9e925-2876-4e83-9b62-1920bece3348","html_url":"https://github.com/fjossinet/Assemble2Docker","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/fjossinet/Assemble2Docker","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fjossinet%2FAssemble2Docker","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fjossinet%2FAssemble2Docker/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fjossinet%2FAssemble2Docker/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fjossinet%2FAssemble2Docker/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/fjossinet","download_url":"https://codeload.github.com/fjossinet/Assemble2Docker/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/fjossinet%2FAssemble2Docker/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28735381,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-24T19:23:36.361Z","status":"ssl_error","status_checked_at":"2026-01-24T19:23:28.966Z","response_time":89,"last_error":"SSL_read: 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":[],"created_at":"2024-11-06T12:19:28.097Z","updated_at":"2026-01-24T19:52:07.253Z","avatar_url":"https://github.com/fjossinet.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"Assemble2Docker\n===============\n\nA docker image containing the following algorithms fully configured:\n\n* [RNAVIEW](http://ndbserver.rutgers.edu/ndbmodule/services/download/rnaview.html)\n* [Vienna RNA package](https://www.tbi.univie.ac.at/RNA/)\n* [foldalign](http://rth.dk/resources/foldalign/)\n* [LocARNA](http://rna.informatik.uni-freiburg.de/LocARNA/)\n\nInstallation\n------------\n\nFirst you need to install Docker on your computer. You can find all the details [here](https://docs.docker.com/engine/installation/).\n\nThen, to get our docker image, you need to type:\n\n    docker pull fjossinet/assemble2\n\nUsages and Examples\n-------------------\n\nIn general, these algorithms need input files. Consequently, you have to mount the file system of your computer (the host) in the Docker container (the guest). This is done with the -v option.\n\nLocARNA algorithm:\n\n     docker run -v /Users/fjossinet/my_files/:/data fjossinet/assemble2 mlocarna /data/my_sequences.fasta\n\nRNAVIEW algorithm:\n\n    docker run -v /Users/fjossinet/my_files/:/data fjossinet/assemble2 rnaview -p /data/my_3D.pdb\n\nRNAFold algorithm:\n\n    docker run -v /Users/fjossinet/my_files/:/data fjossinet/assemble2 bash -c 'RNAfold \u003c /data/my_sequence.fasta'\"\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffjossinet%2Fassemble2docker","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffjossinet%2Fassemble2docker","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffjossinet%2Fassemble2docker/lists"}