Download and Setup

KGGSum and Its Running Resources¶

KGGSum is a Java-based tool distributed as a Java Archive file (kggsum.jar). Depending on the analysis type, additional resource files may be needed:

Gene-based association tests (GATES, ECS) and heritability estimation (EHE) require gene annotations.
Gene-expression causal-effect estimation (EMIC) requires eQTL summary statistics.
Almost all analyses in KGGSum require reference genotypes to estimate linkage disequilibrium of variants.

The following table provides download links for the latest version of KGGSum and its resources:

File	Description	Main Version	Size
kggsum.jar	Core program file	1.0	~32 MB
resources.zip	Resource files (excluding reference genotypes and eQTL data)	1.0	~180 MB
tutorials.zip	Example datasets for tutorials	1.0	~255 MB
	For historical releases

Contents of resources.zip

The resources.zip package provides the essential annotation and coordinate-conversion files used by KGGSum:

File	Description
`resources/liftover/hg19ToHg38.over.chain.gz`	Chain file for converting coordinates from hg19 to hg38
`resources/reference/CanonicalTranscript.txt.gz`	Canonical transcript metadata (gene symbol, Ensembl ID, etc.)
`resources/reference/GEncode_hg38_kggseq_v2.txt.gz`	GENCODE gene annotations (hg38)
`resources/reference/refGene_hg38_kggseq_v2.txt.gz`	RefGene gene annotations (hg38)

💡 KGGSum allows flexible resource usage — you can download only the files needed for your specific analysis.

Installation and Environment Setup¶

KGGSum requires Java Runtime Environment (JRE) 1.8 or higher. You may use either Oracle Java or OpenJDK.

To verify your installation, open a terminal (or Command Prompt on Windows) and run:

java -version

If the output shows a version ≥ 1.8, your Java environment is ready and KGGSum can run normally.

💡 If KGGSum cannot start, check whether Java is added to your system PATH variable.

Also ensure your system meets the recommended hardware specifications, especially for large datasets.

Quick Tutorial Setup¶

Follow these steps to set up a minimal working environment for KGGSum tutorials:

1. Download Required Files: kggsum.jar, resources.zip and tutorials.zip
2. Extract Files: Unzip both resources.zip and tutorials.zip into your preferred directory.
3. Organize Folder Structure: Place all components under one working folder, e.g.:

my-project/
├── kggsum.jar
├── resources/
└── tutorials/

4. Test the Installation

Open a terminal in the tutorials/ directory and run:
```
java -jar ../kggsum.jar
```
If installed successfully, KGGSum will print usage information or help text.

Notes

The resources/ folder contains files necessary for tutorials (e.g., liftover chains, gene annotations).
For advanced analyses, additional resources (e.g., reference genotypes, eQTL summary statistics) may be downloaded separately.