> For the complete documentation index, see [llms.txt](https://clinical-genomics.gitbook.io/project-mip/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://clinical-genomics.gitbook.io/project-mip/develop/documentation/cli.md).

# Cli

MIP uses [MooseX::App](https://metacpan.org/pod/MooseX::App) to create a single command line interface (CLI) entry point to all MIP related processes. The main application is called by:

```bash
$ mip
```

This will show the usage, global parameters and all available commands and subcommands. There is currently three main commands:

* Install
* Analyse
  * rd\_dna
  * rd\_rna
  * rd\_dna\_vcf\_rerun
* Download
  * rd\_dna
  * rd\_rna

There are three levels of parameters:

* Global
* Commands
* Sub commands

These parameters are defined for the CLI at each level of the underlying namespace in `lib/MIP/Cli`. The complete parameter feature is defined for each command and subcommand in definition file located under `definitions`.

A parameter that is unique to a command or subcommand should only be defined once in that namespace and corresponding definitions file.

A parameter that is shared by all subsequent processes only needs to be defined in the parent namespace and corresponding definitions file.