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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 the latest version of KGGA and its resources:

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
For historical releases
Contents of resources.zip

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

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.

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

  1. Download and Install JRE

  2. For Java SE JRE, visit the official Java download page and follow the instructions.

  3. For OpenJDK JRE, refer to the OpenJDK installation guide.

  4. Verify Installation

  5. Open a terminal (Linux/macOS) or Command Prompt/PowerShell (Windows).

  6. Enter the command:

    java -version

  7. 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)

  8. 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:

  1. Download Files

  2. kgga.jar

  3. tutorials.zip

  4. Unzip tutorials.zip

  5. Extract the contents to a directory (e.g., tutorials/).

  6. Place kgga.jar

  7. Copy or move the latest kgga.jar into the tutorials/ directory.

  8. Verify KGGA Installation

  9. Open a terminal (Linux/macOS) or Command Prompt/PowerShell (Windows).

  10. Navigate to the tutorials/ directory:

    cd path/to/tutorials

  11. 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.