Dockerfile-prep-gwas-files

# Build with: docker build -t prep-gwas-files -f Dockerfile-prep-gwas-files .
# Run with:  docker run --volume=/Volumes/stadler/SHCSData/data:/data:ro --volume=`pwd`/output:/output prep-gwas-files

# Base image https://hub.docker.com/_/debian
FROM debian:buster

## Update packages
RUN apt-get update && apt-get -y upgrade

## Install PLINK2: https://www.cog-genomics.org/plink/2.0/
RUN apt-get install -y wget
RUN apt-get install unzip
RUN wget https://s3.amazonaws.com/plink2-assets/alpha2/plink2_linux_avx2.zip
RUN unzip plink2_linux_avx2.zip

## create output directory
RUN mkdir -p output

## Copy in scripts
COPY scripts/ scripts

## run scripts
ENTRYPOINT ["bash", "/scripts/bash/prep-gwas-files.sh"]