gwaslake – convenience containers and documents for exploring the MRC Integrative Epidemiology Unity “gwasglue” ecosystem for GWAS

We are indebted to the University of Bristol MRC Integrative Epidemiology Unit for infrastructure underlying this ecosystem:

dockerhub

This repo includes code for a ‘workshop’ consisting of a docker container and Rmarkdown files that explore the use of this infrastructure. On any internet-connected machine with a docker client, you can use

docker run -ti -e PASSWORD=abc -p 8787:8787 vjcitn/gwaslake:latest

to acquire the docker container image and start it up so that it serves Rstudio at port localhost:8787. There will be a vignettes folder in the working directory, and all software necessary to build the vignettes is already installed in the container.

Note that the MRC IEU gwasglue package is not installed – it has too many dependencies on remote packages in github. However, you can install it and its dependencies manually with remote reference mrcieu/gwasglue.