Build environments

Most MDI pipelines, including those in svx-mdi-tools, depend on third-party programs installed into an appropriate runtime environment. You may use one of two methods to set up your environment.

Singularity containers

Singularity containers are a platform for code encapsulation that is especially useful on shared computing resources (unlike Docker which is not allowed on many shared HPC servers).

For servers and pipelines that support publicly shared Singularity containers you do not need to do anything except agree to downloading the required container when prompted.

The following pipelines currently support singularity containers:

• genomex-mdi-tools/download

Conda environments

Alternatively, 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 download conda --create   # for downloading genome(s), if required
mdi svCapture conda --create  # or replace svCapture with another required pipeline

Defaults and overrides

The MDI utility will recognize if you have Singularity on your server and if the requested pipeline supports containers. If both are true, it will use containers by default. Otherwise, you must build your own conda environment as described above.

You can force the use of locally built environments by setting the --runtime option, e.g.,

mdi svCapture align --runtime conda