Install EPACTS ​

EPACTS 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 to ask general questions about the EPACTS software.

1. Install required packages ​

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

2. Link to the software ​

bash
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 could change to another directory if you prefer

4. Download the code, unpack and clean up ​

bash
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 ​

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

6. Download reference FASTA files from 1000 Genomes FTP ​

bash
$softwaredir/bin/epacts download

7. Run ​

bash
$softwaredir/bin/epacts