# 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.

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

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

# Install required packages

sudo apt update -y && sudo apt-get install -y \
         build-essential \
         ghostscript \
         groff \
         gnuplot \
         zlib1g-dev \
         r-base-core

# Link to software (alternatively, clone the git repo)

software="http://csg.sph.umich.edu/kang/epacts/download/EPACTS-3.2.6.tar.gz"

# Define where to store the software.

Below is a suggestion that you may change.

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

# 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

# Compile using make and make install

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

# Download reference FASTA files from 1000 Genomes FTP

$softwaredir/bin/epacts download

# Run

$softwaredir/bin/epacts

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