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General

General Settings (threads, resources, and updates)

Beyond analysis-specific options, KGGSum provides a set of common settings that affect:

  • how many CPU threads to use,
  • where to find resource data,
  • which chromosomes to consider,
  • whether to update the local kggsum.jar.

There are also additional options for template data and advanced parallel execution (if enabled in your build/version).

Here are the most commonly used general options:

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 https://idc.biosino.org/pmglab/resource/kgg/kggsum/resources/
Note: this option should be placed ahead of the main options. e.g., java -Xmx4g -jar ../kggsum.jar --channel ./resources assoc		 ./resources
--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.		 -