Build environments

Most MDI pipelines, including those in ont-mdi-tools, depend on third-party programs installed into an appropriate runtime environment.

Conda environments

All pipeline environments can be set up using conda, which must be installed and available on your system. You then call the following MDI command(s) to create/build the required environment(s).

mdi ont conda --help 
mdi ont conda --create 
mdi ont conda --list 

mdi modmod conda --create  # etc.

Dorado

The commands above will install pod5 and remora, but dorado is not yet available via conda. However, ont-mdi-tools provides the shared action module download you can use to quickly download Dorado and its associated basecalling modules.