General usage

As described here, data analysis in MDI tool suites is divided into two stages called pipelines, which perform high-performance computing on Linux servers, and apps, which support interactive data visualization in R Shiny.

Methods and help for calling MDI pipelines

Please see the detailed documentation and MDI command help:

mdi --help

for information about the ways you can execute an MDI pipeline on your server. Briefly, you can run a pipeline action as a program from the command line, e.g.:

mdi <pipeline> <action> [options] # e.g., mdi svCapture align

However, rather than specifying options at the command line, we recommend creating a job configuration file and then either calling it directly:

mdi <pipeline> <data.yml> # e.g., mdi svCapture mydata.yml

or, better yet, submitting it to the job scheduler on your HPC cluster:

mdi submit <data.yml> # e.g., mdi submit mydata.yml

Help for assembling job configuration files

Complete instructions for constructing MDI job files are found here - there are many additional helpful features.

• https://midataint.github.io/mdi/docs/job_config_files.html

The following command will print a template you can use to quickly construct a new job file from scratch.

mdi <pipeline> template --help
mdi <pipeline> template > mydata.yml # e.g., mdi svCapture template
nano mydata.yml

Finally, the following commands will give show help for a pipeline or one of its actions to understand how options are organized and what they do:

mdi <pipeline> --help          # e.g., mdi svCapture --help
mdi <pipeline> <action> --help # e.g., mdi svCapture align --help