spiros / docker-ukbiobank-utils

Docker image for running UK Biobank utilities: ukbunpack, ukbfetch, ukblink, ukbgene, ukbmd5, ukbconv, and gfetch

ukbiobank utils

   

About

This is a repo to hold a Docker image for UK Biobank utilities: ukbunpack, ukbfetch, ukblink, ukbgene, ukbmd5, ukbconv By default, UK Biobank will only provide binaries for Linux and Windows for their utilities.
This Docker image will allow you to run them anywhere you want as long as you have Docker (i.e. OS X).

Build

docker build -t ukbiobank-utils .

Run

# Decode
docker run -v $PWD:/data --rm -it spiros123/ukbiobank-utils ukbunpack /data/ukbXXXXXX.enc /data/<keyfile>

# Convert to csv/r/docs/etc
docker run -v $PWD:/data --rm -it spiros123/ukbiobank-utils ukbconv /data/ukbXXXXX.enc_ukb csv