System Requirements and Setup for KGGA

This section provides the system requirements for running KGGA, a Java-based tool for genetic analysis, along with detailed instructions for setting up the Java Runtime Environment (JRE) and downloading necessary resources.

KGGA and Its Running Resources

KGGA is distributed as a Java Archive file (kgga.jar) and requires additional resources, such as reference genes and genomic annotations, for most analyses. Below are the download links for KGGA and its related files:

File	Description	Version	Size
kgga.jar	The KGGA program	1.0	~23 MB
tutorials.zip	Toy input data and minimal resources for tutorials	1.0	~200 MB
resources	Folder with full resource data files (GTB or text format)	1.0	Varies

Update History

2025-5-1 Release the first formal version of KGGA.
2025-6-3 Update the GBC lib of KGGA.

Resource Files in tutorials.zip

The tutorials.zip file includes a resources/ folder with minimal data for gene feature annotation and coordinate conversion:

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

System Requirements

KGGA operates within a Java Virtual Machine (JVM), ensuring compatibility across multiple operating systems. Below are the hardware and software requirements:

Hardware/Software	Requirement
Operating System	Any OS supporting Java (e.g., Linux, macOS, Windows)
Java Runtime Environment	Java SE JRE version 1.8 or higher
CPU	4 cores or more recommended
Memory	16 GB RAM or higher recommended
Free Disk Space	Up to 10 GB for KGGA and associated datasets

Setting Up a Java Runtime Environment (JRE)

KGGA requires a Java Runtime Environment (JRE) version 1.8 or higher. You can use either Java SE JRE or OpenJDK JRE.

Installation Steps

Download and Install JRE
- For Java SE JRE, visit the official Java download page and follow the instructions.
- For OpenJDK JRE, refer to the OpenJDK installation guide.
Verify Installation
- Open a terminal (Linux/macOS) or Command Prompt/PowerShell (Windows).
- Enter the command:
```
java -version
```
- If installed correctly, you should see output like:
  
  Java(TM) SE Runtime Environment (build 1.8.0_XXX)
  
  or
  
  OpenJDK Runtime Environment (build 1.8.0_XXX)
- If the command is not recognized, confirm that the JRE is installed and that the java command is in your system's PATH.

Setting Up an Environment for Quick Tutorials

Follow these steps to set up an environment for running the tutorial examples:

Download Files
- kgga.jar
- tutorials.zip
Unzip tutorials.zip
- Extract the contents to a directory (e.g., tutorials/).
Place kgga.jar
- Copy or move the latest kgga.jar into the tutorials/ directory.
Verify KGGA Installation
- Open a terminal (Linux/macOS) or Command Prompt/PowerShell (Windows).
- Navigate to the tutorials/ directory:
```
cd path/to/tutorials
```
- Run the following command to test KGGA:
```
java -jar kgga.jar
```
  If successful, KGGA will display usage information or a help message.

Notes

The resources/ folder within tutorials/ provides minimal data for tutorials, such as gene annotations and liftover chains.
For more extensive analyses, download additional resources from the resources folder as needed.

General Notes

Ensure your system meets the recommended hardware specifications, particularly for large datasets.
If Java-related issues arise, double-check the JRE installation and PATH configuration.
Advanced analyses may require additional resources (e.g., reference genotypes, annotation databases) available via the provided download links.

results matching ""

No results matching ""