CNVkit needs various dependencies from Python and R, which would otherwise have to be installed in separate manual steps (Supplementary Fig. \ref{491724}c). The above command installs all dependencies needed by CNVkit, including Python and R themselves. Conda enables updating and removing all these dependencies via one unified interface.
A key benefit of Conda is the ability to define isolated, shareable software environments. This can happen ad-hoc, or via YAML (
https://yaml.org) files. For example, the following file defines an environment consisting of Salmon
\cite{Patro2017} and DESeq2
\cite{Love2014}. Here we specify the exact versions to install, though this is not strictly necessary as the latest available version will be installed by default: