Installation

GRAB is an R package, with part of its code written in C++ for improved performance. GRAB can be installed on Linux, Windows, or macOS via CRAN, Conda, or from source code.

Install via CRAN

Install GRAB from CRAN in your R console:

install.packages("GRAB")

Install via Conda

Install GRAB in a new Conda environment named grab_env from the conda-forge channel:

conda create -n grab_env -c conda-forge r-grab

Install from source code

First, create an environment for GRAB using Conda:

conda create --name grab_env --channel conda-forge \
  zlib r-bh r-rcpp r-rcpparmadillo r-rcppparallel r-data.table r-dplyr r-lme4 r-mvtnorm \
  r-ordinal r-survival r-rsqlite r-skat r-remotes r-dbplyr r-igraph r-optparse r-r.utils

Then, activate the environment and install GRAB:

conda activate grab_env
R -e "remotes::install_github('GeneticAnalysisinBiobanks/GRAB', upgrade='never')"

To verify that GRAB was installed successfully, check its version with:

R -e "packageVersion('GRAB')"

Install GRAB with Docker

Build a Docker image for GRAB named grab_img using the following command:

docker build -t grab_img - <<EOF
FROM condaforge/miniforge3
RUN conda install r-grab
EOF

Then, verify that GRAB can be loaded properly in a container:

docker run grab_img R -e "library(GRAB); message('GRAB loaded successfully')"

For instructions on using GRAB with Docker on the UK Biobank Research Analysis Platform (RAP), please see the section UK Biobank RAP.