To create a Docker image:

1. Download gmp and ntl libraries, unpack to directories "gmp" and "ntl" relative to the root of this repo

wget https://ftp.gnu.org/gnu/gmp/gmp-6.1.2.tar.bz2
tar xvvjf gmp-6.1.2.tar.bz2
mv gmp-6.1.2 gmp
wget http://www.shoup.net/ntl/ntl-11.3.0.tar.gz
tar xvvzf ntl-11.3.0.tar.gz
mv ntl-11.3.0 ntl

2. Run the docker build command to create an image called "idash18linreg", which can be uploaded to Docker Hub:

docker build --rm -t idash18linreg .
docker tag idash18linreg idash18ucsd/helinreg
docker push idash18ucsd/helinreg

To run the docker image:

1. Install the docker software

• on Ubuntu/Debian, do apt-get install docker
• on Arch Linux, do pacman -S docker and then systemctl start docker.service
• on Mac, the docker software can be downloaded here https://store.docker.com/editions/community/docker-ce-desktop-mac

2. Now we can pull the uploaded docker image (on linux we must use sudo docker ... but on Mac we can just do docker ... with regular user account):

• To pull and run the docker image for linear regression:

sudo docker pull idash18ucsd/helinreg

sudo docker run -it --rm idash18ucsd/helinreg

• To pull and run the docker image for logistic regression:

sudo docker pull idash18ucsd/helogreg

sudo docker run -it --rm idash18ucsd/helogreg

3. Then we shall see a command line prompt of the docker environment:

root@...:/usr/src/IDASH18/gwas# 

We can run the test program inside the docker environment like this:

root@...:/usr/src/IDASH18/gwas# ./testlinreg idashdata/covariates.txt idashdata/snpMat.txt

We can also run the test program from outside of the docker environment, e.g., in a terminal:

sudo docker run -it --rm \
 -v "$PWD"/IDASH18/gwas/idashdata/covariates.txt:/data/covariates.txt \
 -v "$PWD"/IDASH18/gwas/idashdata/snpMat.txt:/data/snpMat.txt \
 idash18 testlinreg /data/covariates.txt /data/snpMat.txt

The "-v" option mounts a file to a path inside the docker environment. The test programs "testlinreg" and "testlogreg" are copied to /usr/bin/, so we can call it just as "testlinreg" and "testlogreg".