{"id":18989817,"url":"https://github.com/cdcgov/mira","last_synced_at":"2025-04-22T11:11:10.415Z","repository":{"id":152772342,"uuid":"619866272","full_name":"CDCgov/MIRA","owner":"CDCgov","description":null,"archived":false,"fork":false,"pushed_at":"2025-03-25T15:23:16.000Z","size":197511,"stargazers_count":18,"open_issues_count":5,"forks_count":6,"subscribers_count":6,"default_branch":"prod","last_synced_at":"2025-03-25T15:45:27.629Z","etag":null,"topics":["cdc-influenza-division","genome-annotation","genome-assembly","influenza","irma","ncird-id","quality-control","rsv","sars-cov-2"],"latest_commit_sha":null,"homepage":"https://cdcgov.github.io/MIRA/","language":"Python","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/CDCgov.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-03-27T15:11:48.000Z","updated_at":"2025-01-07T04:53:25.000Z","dependencies_parsed_at":"2023-10-12T03:44:25.631Z","dependency_job_id":"165255de-1c93-49f5-9af9-6aa314c42f77","html_url":"https://github.com/CDCgov/MIRA","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":"CDCgov/template","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2FMIRA","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2FMIRA/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2FMIRA/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2FMIRA/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CDCgov","download_url":"https://codeload.github.com/CDCgov/MIRA/tar.gz/refs/heads/prod","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249260473,"owners_count":21239595,"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":["cdc-influenza-division","genome-annotation","genome-assembly","influenza","irma","ncird-id","quality-control","rsv","sars-cov-2"],"created_at":"2024-11-08T17:08:01.187Z","updated_at":"2025-04-22T11:11:10.396Z","avatar_url":"https://github.com/CDCgov.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# \u003cimg src=\"man/figures/logo.png\" align=\"left\" width=\"190\" /\u003e MIRA: Interactive Dashboard for Influenza, SARS-CoV-2 and RSV Assembly and Curation\n\n![pkgdown](https://github.com/cdcgov/mira/workflows/pkgdown/badge.svg)\n![Docker pulls](https://img.shields.io/docker/pulls/cdcgov/mira)\n![Docker image size](https://img.shields.io/docker/image-size/cdcgov/mira)\n![GitHub last commit](https://img.shields.io/github/last-commit/cdcgov/mira)\n\n\u003cbr\u003e\n\n**General disclaimer** This repository was created for use by CDC\nprograms to collaborate on public health related projects in support of\nthe [CDC mission](https://www.cdc.gov/about/organization/mission.htm).\nGitHub is not hosted by the CDC, but is a third party website used by\nCDC and its partners to share information and collaborate on software.\nCDC use of GitHub does not imply an endorsement of any one particular\nservice, product, or enterprise.\n\n\u003chr\u003e\n\u003cbr\u003e\n\n## **Documentation: [https://CDCgov.github.io/MIRA](https://CDCgov.github.io/MIRA)**\n\n### If you've previously installed MIRA and need to upgrade to the latest version, [CLICK HERE](https://CDCgov.github.io/MIRA/articles/upgrading-mira.html)\n\n\u003cbr\u003e\n\n# Overview\n\n**MIRA** is an interactive dashboard created using **[Dash](https://dash.plotly.com/introduction)**, a python framework\nwritten on the top of **Flask**, **Plotly.js** and **React.js**. The dashboard\nallows users to interactively create a metadata and config file for\nrunning Influenza Genome and SARS-CoV-2 Spike-Gene Assembly. Coming soon, it\nwill allow for upload via FTP to NCBI’s databases\n**Genbank**, **BioSample**, and **SRA**, as well as **GISAID**.\n\nMIRA’s dashboard relies on four Docker containers to run its genome assembly and curation:\n\n- **IRMA (Iterative Refinement Meta-Assembler):** designed for the robust assembly, variant calling, and phasing of highly variable RNA viruses. IRMA is deployed with modules for influenza, ebolavirus and coronavirus.\n- **DAIS-Ribosome:** compartmentalizes the translation engine developed for the CDC Influenza Division protein analytics database. The tool has been extended for use with Betacoronavirus.\n- **spyne:** a Snakemake workflow manager designed for running Influenza Genome and SARS-CoV-2 Spike-Gene assembly.\n- **MIRA:** a GUI web interface that allows users to interactively create a metadata and config file for running Influenza Genome and SARS-CoV-2 Spike-Gene assembly and curation.\n\n![](man/figures/MIRA_flowchart_pptx.png)\n\n\u003chr\u003e\n\n## Quick Start on Ubuntu OS\n\n_Need to set up an Ubuntu OS? Follow instructions in [Getting Started.](https://CDCgov.github.io/MIRA/articles/getting-started.html)_\n\n### Install Docker CLI and Docker Compose\n\n```bash\nsudo apt-get update\n```\n\n```bash\nsudo apt-get install ca-certificates curl gnupg lsb-release\n```\n\n- During installation, you will be prompted to enter 'y' or 'n' to proceed. Each time, input 'y' and click `Enter`\n\n```bash\nsudo mkdir -p /etc/apt/keyrings\n```\n\n```bash\ncurl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg\n```\n\n```bash\necho \"deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable\" | sudo tee /etc/apt/sources.list.d/docker.list \u003e /dev/null\n```\n\n```bash\nsudo apt-get update\n```\n\n```bash\nsudo chmod a+r /etc/apt/keyrings/docker.gpg\n```\n\n```bash\nsudo apt-get update\n```\n\n```bash\nsudo apt-get install docker-ce docker-ce-cli containerd.io docker-compose-plugin\n```\n\n5. Verify successful installation\n\n```bash\nsudo docker run hello-world\n```\n\n- This command downloads a test image and runs it in a container. When the container runs, it prints a confirmation message and exits.\n\n### MIRA Container Installation with Docker Compose\n\n- Create a folder called `FLU_SC2_SEQUENCING` to save your sequencing reads to. From the command line, run:\n  \n```bash\nmkdir ~/FLU_SC2_SEQUENCING\n\ncd ~/FLU_SC2_SEQUENCING\n```\n\n- Download the install yml:\n\n```bash\n curl https://raw.githubusercontent.com/CDCgov/MIRA/prod/docker-compose-git.yml | sed \"s%/path/to/data%$(pwd)/%g\" \u003e docker-compose.yml\n```\n\n- Run the install script:\n\n```bash\nsudo docker compose up -d\n```\n\n- [Click here to download tiny test data from ONT Influenza genome and SARS-CoV-2-spike - 40Mb](https://centersfordiseasecontrol.sharefile.com/d-s839d7319e9b04e2baba07b4d328f02c2)\n- [Click here for the above data set + full genomes of Influenza and SARS-CoV-2 from Illumina MiSeqs - 1Gb](https://centersfordiseasecontrol.sharefile.com/d-s3c52c0b25c2243078f506d60bd787c62)\n- unzip the file and find two folders:\n    1. `tiny_test_run_flu`\n    2. `tiny_test_run_sc2`\n- move these folders into `FLU_SC2_SEQUENCING`\n  - if you cannot find the FLU_SC2_SEQUENCING folder in your Linux section of file explorer, look in Linux--\u003ehome--\u003eyour username\n\n- Open your browser and type \u003chttp://localhost:8020\u003e in the address bar.\n- Click `Refresh Run Listing` in MIRA, you should now see these folders listed.\n- Click `Download Samplesheet`.\n  - This will give you an excel sheet with available barcodes populated. Add in our samplenames for ONT data (Illumina data will self identify samplenames based on fastqs)\n- Save the samplesheet and then upload it by clicking on `Drag and Drop your Samplesheet or Click and Select the File`\n- In the dropdown box 'What kind of data is this?', select the correct data type.\n  - If SC2 full genome, also select your primers.\n- Click 'START GENOME ASSEMBLY'\n- Toggle 'Watch IRMA progress' to see IRMA's stdout stream.\n- When \"IRMA is finished!\" is displayed,  Click \"DISPLAY IRMA RESULTS\"\n\n\u003chr\u003e\n\n## Public Domain Standard Notice\n\nThis repository constitutes a work of the United States Government and is not\nsubject to domestic copyright protection under 17 USC § 105. This repository is in\nthe public domain within the United States, and copyright and related rights in\nthe work worldwide are waived through the [CC0 1.0 Universal public domain dedication](https://creativecommons.org/publicdomain/zero/1.0/).\nAll contributions to this repository will be released under the CC0 dedication. By\nsubmitting a pull request you are agreeing to comply with this waiver of\ncopyright interest.\n\n## License Standard Notice\n\nThe repository utilizes code licensed under the terms of the Apache Software\nLicense and therefore is licensed under ASL v2 or later.\n\nThis source code in this repository is free: you can redistribute it and/or modify it under\nthe terms of the Apache Software License version 2, or (at your option) any\nlater version.\n\nThis source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY\nWARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A\nPARTICULAR PURPOSE. See the Apache Software License for more details.\n\nYou should have received a copy of the Apache Software License along with this\nprogram. If not, see \u003chttp://www.apache.org/licenses/LICENSE-2.0.html\u003e\n\nThe source code forked from other open source projects will inherit its license.\n\n## Privacy Standard Notice\n\nThis repository contains only non-sensitive, publicly available data and\ninformation. All material and community participation is covered by the\n[Disclaimer](DISCLAIMER.md)\nand [Code of Conduct](code-of-conduct.md).\nFor more information about CDC's privacy policy, please visit [http://www.cdc.gov/other/privacy.html](https://www.cdc.gov/other/privacy.html).\n\n## Contributing Standard Notice\n\nAnyone is encouraged to contribute to the repository by [forking](https://help.github.com/articles/fork-a-repo)\nand submitting a pull request. (If you are new to GitHub, you might start with a\n[basic tutorial](https://help.github.com/articles/set-up-git).) By contributing\nto this project, you grant a world-wide, royalty-free, perpetual, irrevocable,\nnon-exclusive, transferable license to all users under the terms of the\n[Apache Software License v2](http://www.apache.org/licenses/LICENSE-2.0.html) or\nlater.\n\nAll comments, messages, pull requests, and other submissions received through\nCDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at [http://www.cdc.gov/other/privacy.html](http://www.cdc.gov/other/privacy.html).\n\n## Records Management Standard Notice\n\nThis repository is not a source of government records, but is a copy to increase\ncollaboration and collaborative potential. All government records will be\npublished through the [CDC web site](http://www.cdc.gov).\n\n## Additional Standard Notices\n\nPlease refer to [CDC's Template Repository](https://github.com/CDCgov/template) for more information about [contributing to this repository](https://github.com/CDCgov/template/blob/main/CONTRIBUTING.md), [public domain notices and disclaimers](https://github.com/CDCgov/template/blob/main/DISCLAIMER.md), and [code of conduct](https://github.com/CDCgov/template/blob/main/code-of-conduct.md).\n\n\u003chr\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcdcgov%2Fmira","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcdcgov%2Fmira","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcdcgov%2Fmira/lists"}