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 8NOTE 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/fileExample: --channel /public1/resourcesExample: --channel https://idc.biosino.org/pmglab/resource/kgg/kgga/resources/ |
./resources |
| --cache | Specify the path of the temporary data files. It must be a local file path on the Operating System. Format: --cache path/to/fileExample: --cache ./tmp/ |
[-o]/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 |
--r-server |
Set the address and port number of the R Server. On KGGA, this is required for RUNNER analysis. Format: --r-server host_ip:host_portExample: --r-server localhost:6300 |
[OFF] |
| update | Check and update the local kgga.jar file to the latest version available on the website. Example: java -jar kgga.jar update Note: The update option does not work on Windows. On Windows, you must manually download the latest kgga.jar file and replace the existing one. |
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