GOAL: Genetic Omics Association resolve Linkage Disequilibrium

Step 1: Clone the Repository

First, clone the GOAL repository from GitHub:

git clone https://github.com/vinash85/GOAL.git
cd GOAL

Step 2: Install Dependencies

2.1. Install GSL

First, install the GNU Scientific Library (GSL) using your system’s package manager:

For Ubuntu/Debian:

sudo apt-get update
sudo apt-get install libgsl-dev

or

wget https://mirror.team-cymru.com/gnu/gsl/gsl-latest.tar.gz -O gsl-latest.tar.gz
tar -zxvf gsl-latest.tar.gz
cd gsl-*/
./configure
make
sudo make install

2.2. Install ransampl

Download and install the ransampl library:

wget https://sourceforge.net/projects/ransampl/files/latest/download -O ransampl-latest.tar.gz
tar -zxvf ransampl-1.0.tar.gz
cd ransampl-*/
./configure
make
sudo make install

2.3. Install LAPACK and BLAS

Ensure that LAPACK and BLAS libraries are installed on your system:

For Ubuntu/Debian:

sudo apt-get install liblapack-dev libblas-dev

2.4. Install Required R Packages

Install the necessary R packages:

install.packages(c("BayesLogit", "Rcpp", "RcppArmadillo", "RcppProgress"))

If BayesLogit is not available on CRAN, install it from GitHub:

install.packages("devtools")
devtools::install_github("jwindle/BayesLogit")

Step 3: Modify the Makevars File

Before compiling GOAL, update the Makevars file to include the paths to GSL and ransampl.

1. Navigate to the src/ directory of the GOAL source code.

2. Open Makevars and modify the following lines:

   PKG_CXXFLAGS = -fopenmp -I/usr/local/include -DUSE_R -DNDEBUG -DDISABLE_SINGLE -DNTHROW -DDISABLE_FIO
   PKG_LIBS = -L/usr/local/lib -lgsl -lgslcblas -lm -lransampl -fopenmp -lgomp -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR

   Note: If your libraries are installed in different locations, adjust the paths accordingly.

Step 4: Install the GOAL Package

1. Navigate to the root directory of the GOAL package source code.

2. Run the installation command:

   sudo R CMD INSTALL .

   This will compile and install GOAL into the system-wide R library.

Step 5: Verify the Installation

Open an R session and load the GOAL package to ensure it was installed correctly:

library(GOAL)

If the package loads without errors, the installation was successful.

Troubleshooting

• Missing Dependencies: Ensure all dependencies are installed and paths are correctly set.
• Linker Errors: Double-check the Makevars file for correct paths to GSL, ransampl, LAPACK, and BLAS.
• Package Not Found: Verify that the package is installed in the correct R library path using .libPaths().

Contact

For further assistance, please contact asahu@salud.unm.edu

To speed up the computation GOAL also uses openmp (http://openmp.org/wp/), however this is optional.