{"id":26201982,"url":"https://github.com/dmnfarrell/tracebtb","last_synced_at":"2025-12-24T13:45:10.207Z","repository":{"id":181220044,"uuid":"363664739","full_name":"dmnfarrell/tracebtb","owner":"dmnfarrell","description":"M.bovis WGS surveillance tool.","archived":false,"fork":false,"pushed_at":"2025-02-06T00:04:49.000Z","size":49286,"stargazers_count":2,"open_issues_count":8,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-28T16:43:21.765Z","etag":null,"topics":["epidemiology","geopandas","gis","pyqt5","python","wgs"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","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/dmnfarrell.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGES","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":"2021-05-02T14:01:55.000Z","updated_at":"2025-02-06T00:04:53.000Z","dependencies_parsed_at":"2023-10-22T12:20:39.111Z","dependency_job_id":"1c211c2f-d28d-4410-bc4d-74569378bc62","html_url":"https://github.com/dmnfarrell/tracebtb","commit_stats":null,"previous_names":["dmnfarrell/btbwgstool","dmnfarrell/tracebtb"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmnfarrell%2Ftracebtb","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmnfarrell%2Ftracebtb/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmnfarrell%2Ftracebtb/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmnfarrell%2Ftracebtb/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dmnfarrell","download_url":"https://codeload.github.com/dmnfarrell/tracebtb/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249016625,"owners_count":21198832,"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":["epidemiology","geopandas","gis","pyqt5","python","wgs"],"created_at":"2025-03-12T03:24:35.258Z","updated_at":"2025-09-19T00:16:18.292Z","avatar_url":"https://github.com/dmnfarrell.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# TracebTB\n\n\u003cimg align=\"right\" src=tracebtb/logo.svg width=180px\u003e\n\nThis is a set of applications designed to allow analysis of M.bovis strain types and associated meta data. It integrates genetic, location and cattle movement data for visualisation in a single tool.\n\nThis software is written in Python. It was developed on Ubuntu linux and should run on any linux desktop. The GUI was made using the Qt toolkit using PySide2/PyQt. The web interface was developed with the [Panel](https://panel.holoviz.org/) framework and [Bokeh](https://bokeh.org/) plotting library.\n\n## Usage\n\n### Web application\n\nRun the command `tracebtb-web` from the command line to launch the web application. You should provide a saved project file by using the -p option: `tracebtb-web -p file.tracebtb`. This will launch a web browser window at the address localhost:5010.\n\nSee the [wiki](https://github.com/dmnfarrell/tracebtb/wiki) page for further documentation.\n\n## Installation\n\n### Linux\n\n`pip install -e git+https://github.com/dmnfarrell/tracebtb.git#egg=tracebtb`\n\nNotes: You may need to use pip3 on Ubuntu to ensure you use Python 3. Running this also requires you have **git** installed. The same command can be used to update to the latest version.\n\n### Windows\n\nInstall python as normal. Also install the [git](https://gitforwindows.org/) program if you are to use the githb version. Then use pip from the command shell as above to install. You shouldn't need conda.\n\n## Requirements\n\n* matplotlib\n* pandas\n* geopandas\n* biopython\n* panel\n* bokeh\n* pyside2 or pyqt5/PyQtWebEngine (only for gui)\n\n## Funding\n\nThis tool was developed as part of projects funded by the Irish Department of Agriculture and the Marine (DAFM).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdmnfarrell%2Ftracebtb","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdmnfarrell%2Ftracebtb","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdmnfarrell%2Ftracebtb/lists"}