{"id":23223123,"url":"https://github.com/nextstrain/flu_frequencies","last_synced_at":"2025-10-25T10:10:29.429Z","repository":{"id":71286324,"uuid":"600713930","full_name":"nextstrain/flu_frequencies","owner":"nextstrain","description":"Flu clade and mutation frequencies","archived":false,"fork":false,"pushed_at":"2024-08-26T17:15:05.000Z","size":133227,"stargazers_count":3,"open_issues_count":9,"forks_count":3,"subscribers_count":10,"default_branch":"master","last_synced_at":"2024-08-26T20:22:44.289Z","etag":null,"topics":["clades","flu","influenza","mutations"],"latest_commit_sha":null,"homepage":"https://flu-frequencies.vercel.app","language":"TypeScript","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/nextstrain.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-02-12T11:12:16.000Z","updated_at":"2024-08-26T17:15:08.000Z","dependencies_parsed_at":"2024-08-26T20:39:34.801Z","dependency_job_id":null,"html_url":"https://github.com/nextstrain/flu_frequencies","commit_stats":null,"previous_names":["nextstrain/flu_frequencies"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextstrain%2Fflu_frequencies","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextstrain%2Fflu_frequencies/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextstrain%2Fflu_frequencies/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nextstrain%2Fflu_frequencies/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nextstrain","download_url":"https://codeload.github.com/nextstrain/flu_frequencies/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":230351132,"owners_count":18212790,"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":["clades","flu","influenza","mutations"],"created_at":"2024-12-18T23:16:10.712Z","updated_at":"2025-10-25T10:10:24.391Z","avatar_url":"https://github.com/nextstrain.png","language":"TypeScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Flu frequencies\n\n\u003e Estimating flu clade and mutation frequencies\n\n| branch  | URL                                        |\n|---------|--------------------------------------------|\n| release | https://flu-frequencies.vercel.app/        |\n| master  | https://master-flu-frequencies.vercel.app/ |\n\n## Development\n\nThis README is for the data analysis pipeline. For the web interface, see [web/README.md](web/README.md).\n\n### Setup\n\n#### Using Nextstrain CLI\n\n\u003cdetails\u003e\n\n\u003csummary\u003eCurrently not working due to lack of polars in Nextstrain managed environments (conda/docker)\u003c/summary\u003e\n\n##### Install Nextstrain CLI\n\nOn Linux:\n\n```bash\ncurl -fsSL --proto '=https' https://nextstrain.org/cli/installer/linux | bash\n```\n\nOn macOS:\n\n```zsh\ncurl -fsSL --proto '=https' https://nextstrain.org/cli/installer/mac | bash\n```\n\n##### Setup Nextstrain CLI\n\nYou can set it up to use Docker or a Nextstrain managed conda environment (completely independent of any other conda environments you may have).\n\nUsing docker:\n\n```bash\nnextstrain setup --set-default docker\n```\n\nUsing managed conda environment:\n\n```bash\nnextstrain setup --set-default conda\n```\n\n##### Run analysis\n\nRun analysis:\n\n```bash\nnextstrain build . --profile profiles/flu\n```\n\n\u003c/details\u003e\n\n#### Using custom conda environment\n\nInstall conda environment:\n\n```bash\nmamba env create -f environment.yml\n```\n\nActivate the environment:\n\n```bash\nconda activate flu_frequencies\n```\n\nRun for flu using:\n\n```bash\nsnakemake --profile profiles/flu\n```\n\nRun for SARS-CoV-2 using:\n\n```bash\nsnakemake --profile profiles/SC2\n```\n\n### Viewing results in web app\n\nRun the following command to generate flu frequencies and copy the resulting CSV tables into `data_web/inputs`.\n\n``` bash\nsnakemake prep_web --profile profiles/flu\n```\n\nGenerate the JSON versions of the CSV tables that the web application uses.\n\n```bash\npython scripts/web_convert.py --input-pathogens-json data_web/inputs/pathogens.json --output-dir web/public/data\n```\n\nCommit the updated JSON files in `web/public/data` to a development or base branch and push to GitHub to deploy a Preview version of the web application.\nVercel deploys a web application for each commit in a pull request.\nYou can access each deployment through the repository's [Deployments](https://github.com/nextstrain/flu_frequencies/deployments) page.\n[See the web application README](https://github.com/nextstrain/flu_frequencies/blob/master/web/README.md#branches-release-and-deployment) for more about deployment from the `master` and `release` branches.\n\n### TODO\n\n- Provide mamba environment file for simpler setup\n- Agree on formatters to use (snakefmt and black?)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextstrain%2Fflu_frequencies","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnextstrain%2Fflu_frequencies","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnextstrain%2Fflu_frequencies/lists"}