{"id":19189384,"url":"https://github.com/kvdomingo/primerdriver","last_synced_at":"2025-04-20T06:34:18.545Z","repository":{"id":42026561,"uuid":"237172330","full_name":"kvdomingo/primerdriver","owner":"kvdomingo","description":"PrimerDriver - Automated design of mutagenic PCR primers","archived":false,"fork":false,"pushed_at":"2024-11-08T17:36:18.000Z","size":6651,"stargazers_count":8,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-31T16:58:42.231Z","etag":null,"topics":["biopython","cli","command-line","mutagenic-pcr-primers","polymerase-chain-reaction","primer-design","python","react","site-directed-mutagenesis","web-application"],"latest_commit_sha":null,"homepage":"https://primerdriver.kvd.studio","language":"Python","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/kvdomingo.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-01-30T08:44:53.000Z","updated_at":"2024-11-08T17:35:39.000Z","dependencies_parsed_at":"2024-11-06T14:39:20.895Z","dependency_job_id":null,"html_url":"https://github.com/kvdomingo/primerdriver","commit_stats":null,"previous_names":[],"tags_count":15,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kvdomingo%2Fprimerdriver","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kvdomingo%2Fprimerdriver/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kvdomingo%2Fprimerdriver/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kvdomingo%2Fprimerdriver/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kvdomingo","download_url":"https://codeload.github.com/kvdomingo/primerdriver/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249859688,"owners_count":21335988,"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":["biopython","cli","command-line","mutagenic-pcr-primers","polymerase-chain-reaction","primer-design","python","react","site-directed-mutagenesis","web-application"],"created_at":"2024-11-09T11:29:13.945Z","updated_at":"2025-04-20T06:34:17.503Z","avatar_url":"https://github.com/kvdomingo.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# PrimerDriver: Automated design of mutagenic PCR primers\n\n![PrimerDriver](https://res.cloudinary.com/kdphotography-assets/image/upload/v1587460290/primerdriver/PrimerDriver_logo.png)\n\n![GitHub](https://img.shields.io/github/license/kvdomingo/primerdriver)\n![GitHub release (latest by date including pre-releases)](https://img.shields.io/github/v/release/kvdomingo/primerdriver?include_prereleases)\n![PyPI - Python Version](https://img.shields.io/pypi/pyversions/primerdriver)\n\n## Introduction\n\n_PrimerDriver_ is a user-friendly bioinformatics platform specifically designed to generate primers for site-directed\nmutagenesis experiments into workflows with an easy-to-use command-line interface. “Traversing” PrimerDriver lanes,\nusers can generate possible mutagenic primers upon input of a DNA sequence (`DNA`), design primers for an array of\nspecies codon expression systems through direct mutation of the amino acid (`PRO`), characterize and report\nuser-designed primers (`CHAR`).\n\n## Usage\n\n### A. Running standalone\n\nYou can access and download the CLI from the\n[releases page](https://github.com/kvdomingo/primerdriver/releases). Currently, we only have prebuilt binaries for\n64-bit Windows and Linux. For other OS/architectures, see the section on Building from Source, under Developing Locally.\n\nRun the program in a terminal using\n\n```shell\nprimerdriver -h\n```\n\nThis will run the help program. For first-time users, the program can be run in\ninteractive mode by passing the `-i` flag:\n\n```shell\nprimerdriver -i\n```\n\nThis will walk you through each option step-by-step.\nBatch design can be performed by including\n[`primerdriver`](primerdriver/__main__.py) as part of a shell script.\n\n### B. Running as Python module\n\n#### Prerequisites\n\n- [Git](https://git-scm.com/downloads)\n- [Mise](https://mise.jdx.dev)\n\n#### Setup\n\n1. Clone the repo to your local device and `cd` into it\n    ```shell\n    git clone https://github.com/kvdomingo/primerdriver.git\n    cd primerdriver\n    ```\n\n2. Install dependencies:\n    ```shell\n    mise install\n    ```\n\nRun the program as follows:\n\n```shell\npoetry run python -m primerdriver -h\n```\n\n### C. Running from Docker\n\nRun as follows:\n\n```shell\ndocker run -it --entrypoint python kvdomingo/primerdriver -m primerdriver -h\n```\n\n## Web application\n\nFor a more interactive experience, visit the\n[web application](https://primerdriver.kvd.studio).\n\n## Documentation\n\nThe documentation is available at https://primerdriver-docs.kvd.studio.\n\n## Contributing\n\nOpen a PR or raise an\n[issue](https://github.com/kvdomingo/primerdriver/issues).\nYou may also email Nomer or Kenneth, depending on the nature of the issue.\n\n## Developing locally\n\n### Prerequisites\n\n- [Docker](https://www.docker.com/get-started)\n- [Mise](https://mise.jdx.dev)\n\n### Installing\n\nA step by step series of examples that tell you how to get a\ndevelopment environment running\n\n1. Clone the repo.\n2. Install prerequisites:\n    ```shell\n    mise install\n    pip install -U pre-commit\n    pre-commit install\n    ```\n3. Install backend dependencies:\n    ```shell\n    poetry install --no-root --with dev\n    ```\n4. Run the development servers:\n    ```shell\n    task\n    ```\n\nWait a few minutes for all the containers to start, then access the\nlocal servers in your browser at:\n\n- Web app: http://localhost:3000\n- Docs: http://localhost:8000\n\n### Building from source\n\nRun the script:\n\n```shell\n# On a Linux machine, will build for Linux x64 only\n# On a Windows machine, will build for Windows and Linux x64\ntask build\n```\n\n### Deployment\n\n```shell\ngit add .\ngit commit -m \"DESCRIPTIVE_COMMIT_MESSAGE\"\ngit push origin your_feature_branch\n```\n\nwhere `your_feature_branch` should summarize the changes you are implementing following\nthe [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/) format\n(e.g., `feat/xxxx`, `fix/yyyy`).\n\n## Authors\n\n- **Numeriano Amer \"Nomer\" E. Gutierrez** - Project Lead, Molecular\n  Biologist - [Email](mailto:ngutierrez@evc.pshs.edu.ph) | [GitHub](https://github.com/nomgutierrez)\n- **Kenneth V. Domingo** - Technical\n  Lead - [Email](mailto:kvdomingo@alum.up.edu.ph) | [Website](https://kvd.studio) | [GitHub](https://github.com/kvdomingo)\n- **Shebna Rose D. Fabilloren** - Technical Consultant - [Email](mailto:sdfabilloren@up.edu.ph)\n- **Carlo M. Lapid** - Project Adviser - [Email](mailto:cmlapid@up.edu.ph)\n\n## Versioning\n\nThis project complies with [SemVer](https://semver.org) for versioning. For\nall available versions, see\n[tags](https://github.com/kvdomingo/primerdriver/tags).\n\n## License\n\nThis project is licensed under the [GPLv3 License](./LICENSE).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkvdomingo%2Fprimerdriver","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkvdomingo%2Fprimerdriver","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkvdomingo%2Fprimerdriver/lists"}