This repository contains optimized versions of compute kernels used in genomics applications like GATK and HTSJDK. These kernels are optimized to run on Intel Architecture (AVX, AVX2, AVX-512, and multicore) under 64-bit Linux and Mac OSX.
Kernels included:
GKL release binaries are built on CentOS 7, to enable running on most Linux distributions (see holy-build-box for a good description of portability issues).
Run these commands to set up the build environment on CentOS:
sudo yum install -y java-1.8.0-openjdk-devel git cmake patch libtool automake yasm zlib-devel centos-release-scl help2man
sudo yum install -y devtoolset-7-gcc-c++
source scl_source enable devtoolset-7
After build requirements are met, clone, and build:
git clone https://github.com/Intel-HLS/GKL.git
cd GKL
./gradlew build
For more details check build.sh
implementation
which makes them not accessible by projects depending on GKL unless the project itself also uses those dependencies.
Workaround for this issue is to include following dependencies manually in affected projects:
implementation 'org.broadinstitute:gatk-native-bindings:1.0.0'
implementation 'com.github.samtools:htsjdk:3.0.5'
Fix for this issue is present in master branch.
All code is licensed under the MIT License, except: