STABIX

SETUP

Dependencies

• google test
• fastpfor
• zlib
• cmake
• C++ Standard Library

Setup

git clone git@github.com:kristen-schneider/gwas-cpp.git
cd gwas-cpp
git submodule init
git submodule update

With mamba

mamba env create -f stabix_mamba.yml

Build all

mkdir build
cd build
cmake ..
make

Compile and run COMPRESSION

cd build/
cmake --build . --target gwas_compress
cd ..
./build/bin/gwas_compress config_files/test_config.yml

Compile and run INDEX

cd build/
cmake --build . --target gwas_index
cd ..
./build/gwas_index config_files/test_config.yml

Compile and run DECOMPRESSION

cd build/
cmake --build . --target gwas_decompress
cd ..
./bin/gwas_decompress config_files/test_config.yml

Configuration file

Example configuration file.

See STABIX analysis repository for more analysis and runnign scripts.

---

Generating python bindings

mkdir build
cd build
cmake ..
make stabixpy # python bindings

This does two things:

1. Generates python_package/src/stabix/stabixcore.so
   Import the .so with import stabixpy.
2. Packages for python distribution, python_package/dist.

Note that this triggers compilation for a specific version of python that must be specified in the CMakeLists.txt file. Both version & python executable path must be specified.

Defaults in the CMakeLists.txt file,

SET(PYBIND11_PYTHON_VERSION 3.11.7)
set(PYTHON_EXECUTABLE "/opt/homebrew/bin/python3")