MIP Docker images

This project contains the Docker images used to build the core functionality of the Medical Informatics Platform (MIP).

The images are published on Docker Hub.

The list of images and their purpose is:

Images for the R environment

hbpmip/r-base

Contains a standard R installation. This image is built from parent image ubuntu:17.10.

This image is similar to rocker/r-base but smaller and don't contain r-base-dev package as it brings many heavy dependencies such as gcc which are needed only when installing new packages.

hbpmip/r-mip

Adapt the base R image to the MIP environment.

This image provides a R environment compatible with MIP. See r-mip for details.

hbpmip/r-libs

Contains some standard / usual R packages used in the MIP:

• plyr
• jsonlite
• rjson
• rjstat

Other libraries are already present from r-base such as:

• MASS
• Matrix
• cluster
• foreign
• rpart

This image is built from r-base.

hbpmip/r-java

This image adds OpenJDK 8 and RJDBC. It is built from r-libs.

hbpmip/r-database

This image adds database connectivity. We support RJDBC and some JDBC drivers are installed already for Postgres and Denodo, and RODBC for Postgress.

This image is built from r-java.

hbpmip/r-job

This Docker image layer is the base for workflow jobs executing R scripts.

hbpjdbcconnect R package is installed to simplify getting data in and out of the database.

This image is built from r-database.

hbpmip/r-interactive

This Docker image is functionally similar to r-job, but it is built on top of rocker-r-base and it is significantly bigger. It contains also some additional tools and libraries to make the development of R packages easier.

Building

Pre-requesites

Install Docker engine and captain.

If you are working on the MIP, please use the dev setup scripts. Run ./setup.sh, then select 3) Algorithms developer to have the necessary software installed for you.

Run ./after-git-clone.sh script after cloning this repository to fetch the code for all sub-projects.

Run ./after-update.sh after updating the code for this repository to keep the sub-projects up-to-date.

Build scripts

./build.sh located on the root of this project will attempt to build all images expect the base images. Use ./build.sh --all to build all images including the base images (required the first time you work on this project).

Each folder contains a build.sh script use to create the image defined in the same folder.

Acknowledgements

This work has been funded by the European Union Seventh Framework Program (FP7/2007­2013) under grant agreement no. 604102 (HBP)

This work is part of SP8 of the Human Brain Project (SGA1).