Download and Setup GBC

GBC is an application developed based on Oracle JDK 8. It can be used on any computer device that supports or is compatible with Oracle JDK 8. Users first need to download and install Oracle JDK or Open JDK. For Apple Silicon devices, Zulu JDK can be used as an alternative. In addition, we also provide a Dockerfile to build the runtime image environment for GBC.

Download GBC via wget

# Download GBC
wget http://pmglab.top/gbc/download/gbc-stable-1.0.jar -O gbc.jar

# Run the GBC software package
java -jar gbc.jar

Run GBC through Docker

# Download the Dockerfile file for GBC
wget http://pmglab.top/gbc/download/Dockerfile -O Dockerfile

# Build an image from the Dockerfile file
docker build -t gbc:stable-1.0 .

# Run the GBC software package
docker run -it --rm gbc

# Remove the GBC image and its cache
docker image rm gbc & docker system prune -f

[!TIP|label:Get GBC from Docker Hub|style:callout]

We have built GBC images for amd64 and arm64 using the following commands. You can get them with docker pull suranyi/gbc && docker tag suranyi/gbc gbc:

# Create a multi-platform builder 
docker buildx create --name multibuilder && docker buildx use multibuilder && docker buildx inspect --bootstrap

# Login
docker login

# Push to Docker Registry 
docker buildx build --platform linux/amd64,linux/arm64 -t suranyi/gbc:latest --push .

Memory requirement

GBC has strict memory requirement control. For small-scale genomic data, GBC can usually run with the default memory allocation. For large-scale genomic data, the memory usage of a single thread in GBC does not exceed 2 GB at most. Therefore, we recommend running the GBC program in a heap memory of no less than 4 GB at all times. Users can allocate the runtime heap memory for GBC through the following commands:

java -Xms4g -Xmx4g -jar gbc.jar

When running GBC through Docker, we recommend using the following template command:

# Macos or Linux
docker run -v `pwd`:`pwd` -w `pwd` --rm -it -m 4g gbc

# Windows - cmd
docker run -v `pwd`:/.cache/ -w /.cache/ --rm -it -m 4g gbc

In this statement, -v means that the specified host path is mapped to the container path (host_path: container_path), -w means that the current working path is set (equivalent to running the cd command), -it means that it is run in an interactive terminal, and -m 4g means that the maximum heap size of JVM is set to 4GB.

Updated

The first stable version of GBC is gbc-stable-1.0, with the first code 1 indicating the GTB file architecture version and the second code 0 indicating the functional version. The architecture version is updated when there is a major update to the GTB format architecture such that it is not compatible with the older version. Functional versions are updated only when some high performance computing methods are added.

[!UPDATE|label:2023/04/11|style:callout]

Released stable version 1.0 of GBC. stable version is a fully optimized version that supports all the features of the beta version and provides more friendly and efficient API features.

[!UPDATE|label:2022/06/20|style:callout]

Release a beta version of GBC, version number: version for publication.

• Github Repository: https://github.com/Zhangliubin/gbc
• Online Manual: http://pmglab.top/gbc/history/v1.2