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.

92 Avoid dependency hell and get up and running fast

Microbial Bioinformatics is a rapidly changing field marrying computer science and microbiology. Join us as we share some tips and tricks we’ve learnt over the years. If you’re student just getting to grips to the field, or someone who just wants to keep tabs on the latest and greatest - this podcast is for you. 

The hosts are Dr. Lee Katz from the Centres for Disease Control and Prevention (US), Dr. Nabil-Fareed Alikhan from the University of Oxford (UK), and Prof. Andrew Page from Theiagen Genomics (UK) and bring together years of experience in microbial bioinformatics.

The opinions expressed here are our own and do not necessarily reflect the views of Centres for Disease Control and Prevention, University of Oxford or Theiagen Genomics.

Intro music : Werq - Kevin MacLeod (incompetech.com)
Licensed under Creative Commons: By Attribution 3.0 License
http://creativecommons.org/licenses/by/3.0/

Outro music : Scheming Weasel (faster version) - Kevin MacLeod (incompetech.com)
Licensed under Creative Commons: By Attribution 3.0 License
http://creativecommons.org/licenses/by/3.0/

Question and comments? microbinfie@gmail.com

92 Avoid dependency hell and get up and running fast

Micro Binfie Podcast