{"id":25977650,"url":"https://github.com/juke34/awesome-genome-annotation","last_synced_at":"2025-12-06T01:01:51.546Z","repository":{"id":226063153,"uuid":"767577706","full_name":"Juke34/awesome-genome-annotation","owner":"Juke34","description":"Awesome genome/mitome/plastome/plastidome annotation tool list","archived":false,"fork":false,"pushed_at":"2025-07-25T12:06:34.000Z","size":693,"stargazers_count":6,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-11-03T16:01:52.040Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://juke34.github.io/awesome-genome-annotation/","language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Juke34.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","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,"zenodo":null}},"created_at":"2024-03-05T14:46:32.000Z","updated_at":"2025-07-25T12:06:13.000Z","dependencies_parsed_at":"2024-11-13T18:34:02.714Z","dependency_job_id":"75779d0f-090f-4898-827e-9ddcaf4a6d6e","html_url":"https://github.com/Juke34/awesome-genome-annotation","commit_stats":null,"previous_names":["juke34/awesome-genome-annotation"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/Juke34/awesome-genome-annotation","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Juke34%2Fawesome-genome-annotation","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Juke34%2Fawesome-genome-annotation/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Juke34%2Fawesome-genome-annotation/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Juke34%2Fawesome-genome-annotation/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Juke34","download_url":"https://codeload.github.com/Juke34/awesome-genome-annotation/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Juke34%2Fawesome-genome-annotation/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":27532473,"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","status":"online","status_checked_at":"2025-12-05T02:00:07.920Z","response_time":54,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"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":"2025-03-05T04:38:48.615Z","updated_at":"2025-12-06T01:01:51.507Z","avatar_url":"https://github.com/Juke34.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"[![CC BY 4.0][cc-by-shield]][cc-by]\n\n\n# Awesome genome annotation\n---------------------------\n\nA curated list of awesome genome annotation tools.\nAvailable here [https://juke34.github.io/awesome-genome-annotation/](https://juke34.github.io/awesome-genome-annotation/).  \nPlease feel free to [contribute](CONTRIBUTING.md)!\n\n## Table of Contents\n\n   * [Foreword](#foreword)\n   * [Project layout](#project-layout)\n   * [For collaborators teachers and developers](#for-collaborators-teachers-and-developers)     \n     * [Modify content](#modify-content)   \n     * [MkDocs](#mkdocs)\n        * [Welcome to MkDocs](#welcome-to-mkdocs)\n        * [Installation](#installation)\n          * [Manual](#manual)\n          * [Conda](#conda)\n        * [Testing and building the website](#testing-and-building-the-website)\n\n## Foreword\n\nYou can find here the list of genome annotation tools I have gathered during my bioinformatician life.\nThe data are located into docs/ and the static website made from this repo lives [https://juke34.github.io/awesome-genome-annotation/](https://juke34.github.io/awesome-genome-annotation/).\n\n\n\n## Project layout\n\n```\n    README.md               # General readme \n    mkdocs.yml              # The configuration file for the site rendering.\n    conda_env.yml           # Conda env to build and test the site locally\n    docs/                   # material that will be publish with the static web site\n        Readme.md            # The documentation homepage (Website Home page).\n        pages/              # Folder dedicated to a topic \n            images/         # Folder containing images related to the topic\n            xxx/            # Folder containing the .md files related to the topic topic\n            ...    \n    Images                  # Images used in the README\n```  \n\n## For collaborators teachers and developers\n\nThis part is for collaborators-teachers and developers.\n\n### Modify content\n\nWhen you are in the repository, add and/or modify your markdown tutorials in the docs directory.\nThe arborescence of the website menu is to setup in the `mkdocs.yml` file\n\n### Mkdocs\n\n#### Welcome to MkDocs\n\nFor full documentation visit [mkdocs.org](https://www.mkdocs.org).  \nFor full documentation about the [material mkdocs theme](https://squidfunk.github.io/mkdocs-material/).\n\n#### Installation\n\n##### Manual\n\nAs prerequisite you need python \u003e=3.8 and pip.  \n\nInstall Mkdocs:\n\n`pip install mkdocs`\n\nFor the theme:  \n`pip install mkdocs-material`\n\nFor the extensions:  \n`pip install pymdown-extensions`\n\nFor the plugins:  \n`pip install mkdocs-minify-plugin`  \n`pip install mkdocs-macros-plugin`  \n`pip install mkdocs-embed-external-markdown`\n\n##### Conda\n\nClone the repository and move in it.  \nThen install all dependencies using conda and the `conda_env.yml` shipped with this repo:\n\n```\nconda env create -f conda_env.yml\n```\n\nActivate the environment and you are good:\n\n```\nconda activate education\n```\n\n#### Testing and building the website\n\n\n* `mkdocs serve` - Start the live-reloading docs server, to test the site locally (http://127.0.0.1:8000/).\n* `mkdocs gh-deploy` - Deploys the site on github pages.\n\n* `mkdocs build` - Build the documentation site.\n* `mkdocs new [dir-name]` - Create a new project.\n* `mkdocs -h` - Print help message and exit.\n\n[cc-by]: http://creativecommons.org/licenses/by/4.0/\n[cc-by-shield]: https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjuke34%2Fawesome-genome-annotation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjuke34%2Fawesome-genome-annotation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjuke34%2Fawesome-genome-annotation/lists"}