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Usage

The parsomics-cli is a command line utility (CLI) to operate parsomics, allowing users to manage plugins, databases, configurations, and more. This section of the documentation goes over the subcommands of the CLI.

For simplicity, the name of the executable of the parsomics-cli is parsomics, so all commands start with "parsomics".

Getting help​

Whenever in doubt about using the parsomics-cli, you can append the --help option to any subcommand. For example:

parsomics --help
parsomics database --help
parsomics database create --help

Setting up parsomics​

As mentioned in the Setup, the setup subcommand walks users through the initial setup of parsomics:

parsomics setup start

Managing configurations​

The config subcommand allows users to create, edit, view, and locate configuration files, with the following commands:

parsomics config create
parsomics config edit
parsomics config view
parsomics config locate

By default, these commands will use the user-scoped configuratio file, but you can change that with the --scope option, which can be either "user", "system", or "custom". For example:

  1. To print the path to the system-scoped configuration file (if it exists):

    parsomics config locate --scope system

  2. To create a configuration file at a custom location:

    parsomics config create --scope custom ./parsomics-config/

Managing the database​

The database subcommand allows users to create, start, stop, and delete relational databases, with the following commands:

parsomics database create
parsomics database start
parsomics database stop
parsomics database delete
info

If you already ran the parsomics setup start command, then the database has already been created and started for you. Next time, you will not need to create a new database, only start the existing one with parsomics database start.

Managing plugins​

The plugin subcommand allows users to install, uninstall, list, get information, and even start developing plugins with the following commands:

parsomics plugin install <plugin-name>
parsomics plugin uninstall <plugin-name>
parsomics plugin list
parsomics plugin info <plugin-name>
parsomics plugin create <tool-name> <plugin-directory>

Read more about plugin development in the Writing plugins section.

Running the analysis​

The analysis subcommand allows users to start and check the status of analyzes, that is, the process through which parsomics processes all configured files and inserts their data in the relational database.

You can set the path of the configuration file that should be used for any given analysis run, like so:

parsomics analysis run ./parsomics-config/contig.toml

If no path is given, configuration file resolution is used to pick one.

info

The database must have been started before you run the parsomics analysis. For that, make sure you run parsomics database start before you run parsomics analysis run.