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Using docker
First, you need to install docker on your computing system. Here are some guides to install it:
- Ubuntu: https://www.hostinger.com/tutorials/install-docker-on-ubuntu/
- Mac OSX: https://docs.docker.com/docker-for-mac/install/
Once you have docker installed and running, you can use the following command to build the image which uses the DockerFiles in the Github repository.
git clone https://github.com/rgcgithub/regenie
cd regenie
make docker-build ## Add 'HAS_BOOST_IOSTREAM=1' and/or 'STATIC=1 MKLROOT=/root/' to compile with Boost Iostream/Intel MKL
This will build the Regenie docker image and you can check the list of available images using
docker image ls
Alternatively, you can pull the image from the Github repository. You will first need to authenticate to GitHub Container Registry using your Github personal access token, which can be obtained following these instructions.
Once you have the token which we assume is saved in the file 'GH_TOKEN.txt', you can authenticate using
cat GH_TOKEN.txt | docker login ghcr.io -u USERNAME --password-stdin
where USERNAME corresponds to your GitHub username.
Finally, you can pull the image (located here) using
docker pull docker.pkg.github.com/rgcgithub/regenie/regenie:v1.0.6.7.gz
Sample regenie commands are included in the script 'test/test_docker.sh' in the Regenie source directory. To run these, you can use
make docker-test ## Add 'HAS_BOOST_IOSTREAM=1' and/or 'STATIC=1 MKLROOT=/root/' if compiled with Boost Iostream/Intel MKL
If no issues are encountered, you should see a template command for running Regenie with docker at the end
docker run -v $(MOUNT_DIR):/docker/ regenie:v1.0.6.7 regenie ...