This repository contains a docker-compose file for extending the ISB CGC RStudio example image with tools for creating Next-Generation Clustered Heat Maps (NG-CHMs). The docker-compose file extends the ISB image with the NGCHM R package and a small package (ISB-CGC-utils) containing example functions for creating NG-CHMs using data obtained from the ISB CGC cloud pilot.
This system is designed to run on on any machine running Docker and Docker Compose. The machine concerned can be local to your environment or in any cloud environment that supports Docker (including but not limited to the Google Compute Engine). It is not designed for the Google Container engine.
Clone this repository to a machine running Docker version 10 or higher and Docker Compose version 1.6.2 or higher.
The system uses a named docker volume to store RStudio data:
$ docker volume create --name=rstudioDataCd into the repository and start the docker containers:
$ cd rstudio-isb-ngchm-demo
$ docker-compose up -dThe container will publish the rstudio interface on port 8787.
In a cloud environment you might need to enable access to that port.
This system must be used in conjunction with one or more NG-CHM systems.
The ngchm-system-one repository contains a docker-compose file for creating a ready-to-use NG-CHM system.
Once up and running, the home page for that server will provide instructions for connecting it with this RStudio system. The R package documents how to create NG-CHMs.