Update README

README.md

@@ -4,27 +4,52 @@
 # Genomics Kernel Library (GKL)
 This repository contains optimized versions of compute kernels used in genomics applications like
 [GATK](https://github.com/broadinstitute/gatk) and [HTSJDK](https://github.com/samtools/htsjdk). These kernels are
-optimized to run on Intel Architecture under 64-bit Linux and Mac OSX.
+optimized to run on Intel Architecture (AVX, AVX2, AVX-512, multicore, and FPGA) under 64-bit Linux and Mac OSX.
 
 Kernels included:
-* **PairHMM**: AVX optimized version of the PairHMM algorithm, which is used to perform pairwise alignment of reads vs. haplotypes
-in GATK HaplotypeCaller and MuTect2
-* **igzip compression**: High performance level 1 compression optimized for genomic data
-* **otc_zlib compression**: Optimized zlib compression for level 2 through 9
+* **PairHMM**
+  * AVX and AVX-512 optimized versions of PairHMM used in GATK HaplotypeCaller and MuTect2. 
+  * OpenMP support for multicore processors.
+  * FPGA support for [Intel PAC](https://www.altera.com/products/boards_and_kits/dev-kits/altera/acceleration-card-arria-10-gx.html) and select vendor cards.
+* **Smith-Waterman**
+  * AVX2 and AVX-512 optimized versions of Smith-Waterman used in GATK HaplotypeCaller and MuTect2.
+* **DEFLATE Compression/Decompression**:
+  * Performance optimized Level 1 and 2 compression and decompression from Intel's [ISA-L](https://github.com/01org/isa-l) library.
+  * Performance optimized Level 3 through 9 compression from Intel's [Open Source Technology Center](https://01.org/) [zlib](https://github.com/jtkukunas/zlib) library.
+
+# Building GKL
+GKL release binaries are built on CentOS 6 to enable running on most Linux distributions (see [holy-build-box](https://github.com/phusion/holy-build-box#problem-introduction) for a good discription of portability issues).
 
 ## Requirements
-* Java 8
+* Java JDK 8
+* Git >= 2.5
+* CMake >= 2.8.12.2
+* GCC g++ >= 5.3.1
+* GNU patch >= 2.6
+* GNU libtool >= 2.2.6
+* GNU automake >= 1.11.1
+* Yasm >= 1.2.0
+* zlib-devel >= 1.2.7
+
+## Setup
+Run these commands to setup 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
+sudo yum install -y devtoolset-4-gcc-c++
+source scl_source enable devtoolset-4
+```
 
-## Quickstart
-Clone, build, and test:
+## Build and Test
+After build requirements are met, clone, build, and test:
 ```
 git clone https://github.com/Intel-HLS/GKL.git
 cd GKL
 ./gradlew test
 ```
 
-## License
+# License
 All code is licensed under the [MIT License](https://opensource.org/licenses/MIT), except:
 * PairHMM code from GATK is licensed under the [BSD 3-Clause License](https://opensource.org/licenses/BSD-3-Clause).
+* ISA-L code is licensed under the [BSD 3-Clause License](https://opensource.org/licenses/BSD-3-Clause).
 * Intel Open Source Technology Center zlib (otc_zlib) code is licensed under the [Zlib License](https://opensource.org/licenses/Zlib).
 * zlib code is licensed under the [Zlib License](https://opensource.org/licenses/Zlib).