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.

• 1. Install required packages
• 2. Link to the software
• 3. Define where to store the software.
• 4. Download the code, unpack and clean up
• 5. Compile using make and make install
• 6. Download reference FASTA files from 1000 Genomes FTP
• 7. Run

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

2. Link to the software

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