3. User interface

3.1. Command line interface

Once FATSLiM is correctly installed and configured, it is available from the command line interface by launching the main (and only) executable: fatslim.

3.1.1. Usage

The user interface for FATSLiM is pretty straightforward: simply type fatslim followed by the command you want to use. For example, fatslim version will display detailed information about FATSLiM installation such as versions used for dependencies.

3.2. General commands and options

3.2.1. General options

These options will take precendence over any subsequent command. For instance fatslim --help apl will display help about the apl command and exit, area per lipid calculation will not be done.

3.2.1.1. --help / -h

fatslim --help or fatslim -h without any command will display general help.

Note

fatslim alone (i.e. without any command specified) will also default to displaying help.

If a command a specified (e.g. fatslim -h thickness), the help message for this command will be displayed.

3.2.1.2. --version

fatslim --version will display detailed information about FATSLiM installation (Python, Cython or NumPy versions, Number of threads available, etc...).

Note

This is an alias of the version command.

3.2.2. General commands

These commands do not refer to any analysis.

3.2.2.1. help

fatslim help is just an alias for --help / -h. So fatslim help will display general help and fatslim help command will display help for a specific command.

3.2.2.2. version

fatslim version is just an alias for --version.