# Install EPACTS

EPACTS (opens new window) is a software pipeline to perform various statistical tests for identifying genome-wide association from gwas and sequence data.

This page describes specific steps for setting up EPACTS in your lab on HUNT Cloud.

General questions about EPACTS

Contact Hyun Min Kang (hmkang@umich.edu) at the University of Michigan or join the EPACTS Google group (opens new window) to ask general questions about the EPACTS software.

# 1. Install required packages

sudo apt update -y && sudo apt-get install -y \
         build-essential \
         ghostscript \
         groff \
         gnuplot \
         zlib1g-dev \
         r-base-core
software="http://csg.sph.umich.edu/kang/epacts/download/EPACTS-3.2.6.tar.gz"

You may alternatively clone the git repo.

# 3. Define where to store the software.

softwaredir="/mnt/work/software/epacts/"
mkdir -p $softwaredir

The above path is a suggestion that you may change.

# 4. Download the code, unpack and clean up

wget $software -O $softwaredir/software.tgz
tar -xvzf $softwaredir/software.tgz  -C $softwaredir/
mv -v $softwaredir/EPACTS-3.2.6/* $softwaredir/
rm -rf $softwaredir/EPACTS-3.2.6/
rm $softwaredir/software.tgz

# 5. Compile using make and make install

cd $softwaredir
./configure --prefix=$softwaredir
make
make install

# 6. Download reference FASTA files from 1000 Genomes FTP

$softwaredir/bin/epacts download

# 7. Run

$softwaredir/bin/epacts
Last Updated: 6/17/2024