Instructions for running in Docker

Introduction

Below are details of how to get the CollateralVulnerability2016 R package running inside a docker container. This is useful because it removes any machine or platform-specific dependencies or issues that may cause problems when running the pipeline and makes the pipeline more portable.

Step-by-step instructions

Make a VM with enough RAM and CPU - docker-machine create --driver virtualbox --virtualbox-cpu-count 4 --virtualbox-memory “12024” bigvm

Set big VM as default: eval $(docker-machine env bigvm)

Launch a new docker container from bioconductor - docker run -d -p 8787:8787 bioconductor/release_core

Get the IP address of the docker machine: docker-machine ip bigvm

Can then log into rstudio on VM as rstudio/rstudio: http://ip-address:8787/

Launch a bash session on a running container: docker exec -it bash

Launch R and install packages source("https://bioconductor.org/biocLite.R") biocLite() biocLite(c('GOSemSim', 'biomaRt', 'ensembldb', 'EnsDb.Hsapiens.v79', 'RTCGA')) install.packages(c('dplyr', 'tidyr', 'shiny', 'BiSEp', 'devtools', 'readr', 'DT')) devtools::install_github('chapmandu2/CollateralVulnerability2016')

Come out of R into bash to install ruby and intermine gem apt-get install ruby-full gem install intermine

You will now have a virtual machine running a docker container that can run the CV pipeline successfully. See Docker website for more details...

To do:

• Implement as dockerfile
• Share volumes