{"id":18990207,"url":"https://github.com/cdcgov/lpsubp","last_synced_at":"2025-04-16T17:31:45.946Z","repository":{"id":37607377,"uuid":"211335582","full_name":"CDCgov/LpSubP","owner":"CDCgov","description":"LpSubP is a rapid subtyping tool for Legionella pneumophila with core gene set","archived":true,"fork":false,"pushed_at":"2022-06-21T22:54:56.000Z","size":51510,"stargazers_count":1,"open_issues_count":2,"forks_count":7,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-10T19:54:12.754Z","etag":null,"topics":["bioinformatics","coregene","dendrogram","heatmap","jupyter-notebook","legionella","matplotlib","pipeline","python","subtyping"],"latest_commit_sha":null,"homepage":"","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":"change_header.py","contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-09-27T14:18:43.000Z","updated_at":"2023-12-04T14:12:50.000Z","dependencies_parsed_at":"2022-08-18T07:55:42.349Z","dependency_job_id":null,"html_url":"https://github.com/CDCgov/LpSubP","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2FLpSubP","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2FLpSubP/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2FLpSubP/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CDCgov%2FLpSubP/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CDCgov","download_url":"https://codeload.github.com/CDCgov/LpSubP/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249260482,"owners_count":21239598,"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":["bioinformatics","coregene","dendrogram","heatmap","jupyter-notebook","legionella","matplotlib","pipeline","python","subtyping"],"created_at":"2024-11-08T17:09:12.803Z","updated_at":"2025-04-16T17:31:40.937Z","avatar_url":"https://github.com/CDCgov.png","language":"Python","readme":"# Legeonella pneumophila Subtyping Pipeline(LpSubP)\n\nYou can run pipeline through \n\n1) Clone git repository \n\n2) Dockerimage without clone repository\n\n## Getting Started for github\n\nThese instructions will get you a copy of the project up and running on your local machine for development and testing purposes.\n\n### Prerequisites\n\nmodule load Python/3.7\n\nmodule load ncbi-blast+/LATEST\n\nmodule load muscle/3.8.425\n\nmodule load raxml/8.2.9\n\nmodule load Entrez/E-utilities\n\nmodule load prodigal/2.63\n\npip install -r requirements.txt --user\n\n## Quick Start for Git\n\n\n``` \ngit clone https://github.com/CDCgov/lpsubp.git\n\ncd ~/lpsubp/\n\npython pipe1.py ~/50scheme/test1/\n\n```\n\n## Quick start for Dockerfile\n\n### singularity\n\n``` \n\nmodule load singularity\n\nsingularity pull docker://supark87/dockerfile_gittest\n\nsingularity run -B $(pwd)/inputfile/://data/inputfile/(space here)dockerfile_gittest.simg(spacehere)//data/inputfile\n\n``` \n\n### Docker\n\n``` \n\ndocker pull supark87/dockerfile_gittest\n\ndocker run -it -v $(pwd)/inputfile/:/data/inputfile/ supark87/dockerfile_gittest /data/inputfile/ \"your email inside of quotes\"\n\n\n``` \n\n\n\n\nThis script runs entire pipeline from the beginning and get all output results\n\n*base_dir: type 'pwd' in your home directory(i.e./scicomp/home/youruserid/) \n\nThere would be \"outputfile\" directory at the end of pipeline under\n\"your_home_directory/your_genome_directory\" (i.e./scicomp/home/youruserid/test1/outputfile/)\n\nThere would be myscript.log in your home directory that you can check when the pipeline started, each step completed, and finished. \n\n\n## Authors\n\nSubin Park\n\nAPHL fellow at Centers for Disease control and Prevention\n\nPhone : +1 470 725 5110\nEmail :nej1@cdc.gov\n\n## Public Domain \n\nThis repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.\n\n## License Standard Notice \n\nThe repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.\nThis source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.\nThis source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details.\nYou should have received a copy of the Apache Software License along with this program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html\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 information. All material and community participation is covered by the Surveillance Platform Disclaimer and Code of Conduct. For more information about CDC's privacy policy, please visit http://www.cdc.gov/privacy.html.\n\n\nAll comments, messages, pull requests, and other submissions received through CDC including this GitHub page are subject to the Presidential Records Act and may be archived. Learn more at 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 collaboration and collaborative potential. All government records will be published through the CDC web site.\n\n## Additional Standard Notices\n\nPlease refer to CDC's Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcdcgov%2Flpsubp","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcdcgov%2Flpsubp","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcdcgov%2Flpsubp/lists"}