Install

Precompiled binary

The precompiled binary for Linux systems can be downloaded from GitHub. This is the simplest method and will work for most users.

Build from source

Obtain source

git clone git@github.com:MRCIEU/varGWAS.git
cd varGWAS

Load compiler (may be necessary on HPC systems). Tested with GCC v7 & v9.

# BlueCrystal Phase 4
module load languages/gcc/9.3.0
module load tools/cmake/3.20.0

Build dependencies

bash lib.sh

Configure cmake

mkdir -p build
cd build

# use default compiler path
cmake .. -DCMAKE_BUILD_TYPE=Release

### OR ###

# use custom compiler path
CC=/mnt/storage/software/languages/gcc-9.3/bin/gcc \
CXX=/mnt/storage/software/languages/gcc-9.3/bin/g++ \
cmake .. -DCMAKE_BUILD_TYPE=Release

Build

make

Run

./bin/varGWAS

Docker

Image

# pull image from Dockerhub
docker pull mrcieu/vargwas
### OR ###
# Build image from source
docker build -t vargwas .

Run

docker run \
-it \
-v $PWD:/home \
mrcieu/vargwas