Context

In the ongoing installation documentation revolution, the initial thought was to de-duplicate installation instructions and have subprojects reference the central installation guide.

This has already been done with ncov: Setup and installation. However, the new page leads to confusion such as #93. Users are redirected to the central installation docs and follow all the steps there, thinking they are done with installation once finished with that page. They are likely to miss the additional note for native runtime:

Possible solutions

1. Avoid extra installation steps
   • This is how Docker runtime is handled – it already installs ncov-specific tools that are the reason for additional installation with native runtime.
2. Copy the same installation guide into the project installation page. This would go back to the old model with duplication issues such as getting out of sync.
3. For Snakemake workflows, use the --use-conda flag. This would point to the conda environment YAML checked into the workflow-specific repos (e.g. nextstrain.yaml in ncov).