CHAPTER 19: Cross-platform Software Development and Distribution with Bioconda and BioContainers

Bioinformatics software development has become a cornerstone in modern biology research. Large-scale quantitative biology studies have created a demand for more complex workflows and data analysis pipelines. Challenges in reproducing bioinformatics analyses are compounded by the fact that the programs themselves are difficult to install on computers because they rely on software libraries, compilers, and other files, and environment variables collectively called dependencies that are assumed to be available and, thus, are often poorly documented. The Bioconda and BioContainers community have created a complete ecosystem that allow bioinformatics software to be installed and executed under an isolated and controlled environment. Also, it provides infrastructure and basic guidelines to create and distribute bioinformatics containers with a special focus on omics technologies. These cross-platform containers can be integrated into more comprehensive bioinformatics pipelines and different architectures (e.g. HPC or Clouds). In this chapter, we explain how the Bioconda and BioContainers communities can improve reproducibility and deployment in modern large-scale data analysis.