ErmineJ has a simple command line interface (CLI). In addition to providing a scriptable interface to the software, it provides access to some features that are not accessible through the graphical user interface (GUI). The CLI can also be used to start the GUI.

To access the CLI, you need to have installed the generic bundle. See the instructions.

Once you have set up the package, you should be able to access ermineJ by running ermineJ.bat or ermineJ.sh.

OPTIONS
	The following options are supported:

	-a file ...
		Sets the annotation file to be used.

	-F format (--format)		Set format (default is our own; 'affy' is other valid value)	-c file ...
		Sets the class file to be used.

	-d dir ...
		Sets the data folder to be used.

	-e int ...
		Sets the column in the score file to be used for scores.

	-f die ...
		Sets the class folder to be used.

	-g int ...
		Sets the gene replicant treatment:  1 (best gene score used) or  2 (mean gene score used).

	-b Sets 'big is better' option for gene scores (default is false).

	-h or --help
		Shows help.

	-i int ...
		Sets the number of iterations.

	-l {0/1} ...
		Sets whether or not to take logs (default is true).

	-m int ...
		Sets the raw score method:  0 (mean),  1 (quantile), or  2 (mean above quantile).

	-n int ...
		Sets the analysis method:  0 (ORA),  1 (resampling of gene scores),  2 (profile correlation),  3 (ROC), 4 (T-test), 5 (Kolmogorov-Smirnov test)[not all methods may be implemented]

	-o file ...
		Sets the output file.

	-q int ...
		Sets the quantile.

	-r file ...
		Sets the raw file to be used.

	-s file ...
		Sets the score file to be used.

	-t double ...
		Sets the pvalue threshold.

	-x maximum class size ...
		Sets the maximum class size.

	-y minimum class size ...
		Sets the minimum class size.

	-M method or --mtc method
		Sets the multiple test correction method: 0 = Bonferonni,  1 = Westfall-Young (slow),  2 =  Benjamini-Hochberg (default)

	-C file ... or --config file ...
		Sets the configuration file to be used.

	-G or --gui
		Launch the GUI.

	-S file ... or --save file ...
		Save preferences in the specified file.

Configuration files and the command line

Note that this behavior has changed in recent versions of ermineJ. Please note that when running ermineJ from Webstart or the Windows installed version, changes in the gui (graphical user interface) are immediately reflected in the default configuration file stored in your home directory.

• If you don't specify a configuration file, all the options must be supplied on the command line. In previous versions, the configuration file would be read in by default.
• If you do specify a configuration file, options can be overridden on the command line, but they will not be written into the config file.
• If you don't specify a configuration file and use -G to start the gui, the default configuration file will be written and used as usual: it will be modified by other options you pass in or change in the gui.
• If you do specify a configuration file and use -G to start the gui, the specified config file will NOT be modified.

This allows a consistent reuse of the customized config files, if so desired.