{"repo":"shenwei356/perfect-bioinformatic-tools","free":true,"listed":false,"github":"https://github.com/shenwei356/perfect-bioinformatic-tools","clone":"git clone https://github.com/shenwei356/perfect-bioinformatic-tools.git","description":"What should perfect bioinformatic tools be like?","language":null,"stars":159,"topics":["bioinformatics","cli","usability"],"license":"CC0-1.0","category":"cli-tools","readme_excerpt":"Perfect bioinformatic tools What should perfect bioinformatic tools be like? This page lists some personal suggestions for improving the usability of bioinformatic (command-line) tools. General principles - Accurate . This should be the most essential aspect, at least for simple analysis. While there may be occasional bugs, regular updates and bug fixes will make the tool more accurate and reliable over time. - Reproducible . That means users can reproduce the same result with the same input data, the same version of the tool, and the same parameters (assuming the program is deterministic). - Installable . Some tools run perfectly on developers' computers, while users with different platforms might struggle to install them, the failure might be due to different dependencies, hard-coded paths, etc. - User-friendly . A tool should be easy to use, with comprehensive documents and well-handled configuration/input/output. - Long-time maintenance . Bug fixes, adding new features, accuracy and usability improvement. Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software. Installation Basic - Specifying dependencies . - Specifying the lowest version AND the highest version. For example, some standard libraries in Python 3.10 have compatibility problems. - Providing sample/test data . To verify that the tool is successfully installed. Recommended to provide all ways: - Supporting Conda/Pip . IMO, this should be a man","default_branch":null,"files":null,"tree":[],"storefront":"/r/shenwei356","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/shenwei356/perfect-bioinformatic-tools/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}