92 - Avoid dependency hell and get up and running fast

Micro binfie podcast

Often the hard part of bioinformatics isnt the analysis, its getting all of the software you need setup and installed. Come with us on this journey and avoid dependancy hell. In the MicroBinfie podcast, the hosts discuss the struggles of installing, managing, and dealing with dependencies with bioinformatics software. In the past, software installations were a nightmare, and it was common to edit lines of code and manage dependencies manually, causing conflicts like diamond dependency. To ease this process, the hosts suggest using containers, virtual machines, and local environments. They stress the importance of adhering to semantic versioning guidelines and understanding the end-users' perspective for proper documentation, testing, and clarity regarding dependencies. Additionally, software maintenance is critical for its longevity and usability. The hosts also discuss software dependency management with different chip architectures and operating systems. The M1 Apple architecture's differences from traditional computer processors cause compatibility issues and slow down emulation, leading to difficulties in informatics. Using separate Conda environments for each project or Mamba as a package manager can solve dependency-related problems that can cause significant issues. However, Mamba may take shortcuts and create conflicts with specific programs. Other package managers like Homebrew and APT are also discussed. The episode also covers the benefits of using Docker and Singularity to manage software packages on a local machine. Docker is useful for databases, web servers, and complicated pipelines, while Singularity is perfect for more complex software and plays better with HPC. The hosts provide tips on using containers or virtual machines in a team environment, passing containers instead of binary files, and using Docker and Singularity as tools to ease the process. Overall, the episode offers practical advice to streamline the workflow of researchers who manage software packages.