Installation

Table of Contents

fastGxE is a C++ command-line tool for genome-wide genotype-by-environment analysis. This page describes two installation paths:

  • use the prebuilt Linux executable
  • build fastGxE from source with CMake

1. Prebuilt Linux executable #

A prebuilt 64-bit Linux executable is available here: fastGxE Linux Executable

After downloading it, make it executable and check that it runs:

chmod +x fastgxe
./fastgxe -h

This is the quickest option if you only need to run the program and your system is compatible with the published binary.

2. Build from source #

Building from source is recommended when you want to modify the code, change compiler settings, or adjust library paths for your local environment.

Prerequisites #

The current build system expects:

  • a C++17 compiler
  • CMake 3.16 or newer
  • Intel oneAPI compiler and Intel MKL
  • OpenMP support

The repository already vendors several dependencies under external/, including:

  • GSL
  • Eigen
  • LBFGSpp
  • CLI
  • spdlog
  • Boost

Clone the repository # 

git clone https://github.com/chaoning/fastGxE.git
cd fastGxE

Check and update build paths #

Before compiling, review CMakeLists.txt and update the local paths if needed. In particular, these variables often need to match your machine:

  • CMAKE_CXX_COMPILER
  • COMPILERROOT
  • MKLROOT
  • GSLROOT
  • EIGENROOT

The current project configuration is written for an Intel oneAPI-based environment. If you build with a different compiler or install location, adjust the compiler and library paths first.

Configure and compile #

Create a separate build directory and compile with CMake:

mkdir -p build
cd build
cmake ..
cmake --build . -j

The main executable will be generated as:

./fastgxe

If you are in the repository root instead of the build/ directory, run:

./build/fastgxe -h

Static linking option #

The project currently enables full static linking by default through:

FASTGXE_FULL_STATIC_LINK=ON

To keep the default static-link behavior:

cmake .. -DFASTGXE_FULL_STATIC_LINK=ON
cmake --build . -j

If static linking is not available on your system, switch to dynamic linking:

cmake .. -DFASTGXE_FULL_STATIC_LINK=OFF
cmake --build . -j

You can inspect the resulting binary with:

file ./fastgxe
ldd ./fastgxe

3. Quick validation #

After compilation, confirm that the executable starts correctly:

./fastgxe -h

If you want a minimal end-to-end smoke test, the example files in example/ can be used together with the commands shown in the tutorial page.

4. Troubleshooting #

  • If CMake cannot find MKL or the Intel compiler, recheck the path variables in CMakeLists.txt.
  • If static linking fails, rebuild with -DFASTGXE_FULL_STATIC_LINK=OFF.
  • If you changed compiler or dependency paths, it is usually safest to remove the old build/ directory and configure again from scratch.
  • If the executable starts but fails at runtime, verify that the compiler, MKL, and OpenMP settings are consistent with your local environment.