General Setting

There are also some options for resource file paths, template data, and parallel tasks.

Option	Description	Default
`--threads`	Specify the number of threads on which the program will be running. Format: `--threads <int>` Example: `--threads 8` NOTE: As a rule of thumb, please do not give a thread number larger than the number of CPU cores. Too many threads may even slow down the analysis.	4
--channel	Specify the path of resource data files. It could be a local system file path, an intranet file path, or even an internet one. Format: `--channel path/to/file` Example: `--channel /public1/resources`	./resources https://pmglab.top/kggsum/resources
--cache	Specify the path of the temple data files. It must be a local file path on the Operating System. Format: `--cache path/to/file` Example: `--cache ./tmp/`	[--output]/tmp/
--chromosome-tag	Specify the recognizable chromosomes. By default, it only considers the standard chromosomes, 1, ..., 22, X, Y, and M.	1,...,22,X,Y,M
update	Check and update the local kggsum.jar file to the latest version available on the website. Example: `java -jar kggsum.jar update` Note: The update option does not work on Windows. On Windows, you must manually download the latest kggsum.jar file and replace the existing one.	-

General