https://github.com/lren-chuv/r-base-docker-images
Docker images used to integrate the algorithms provided for the Medical Informatics Platform (MIP)
https://github.com/lren-chuv/r-base-docker-images
algorithm-factory docker-images
Last synced: 3 months ago
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Docker images used to integrate the algorithms provided for the Medical Informatics Platform (MIP)
- Host: GitHub
- URL: https://github.com/lren-chuv/r-base-docker-images
- Owner: LREN-CHUV
- License: apache-2.0
- Created: 2016-02-02T12:55:14.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2019-04-09T17:11:48.000Z (over 6 years ago)
- Last Synced: 2025-03-12T22:16:39.606Z (7 months ago)
- Topics: algorithm-factory, docker-images
- Language: Shell
- Homepage:
- Size: 2.56 MB
- Stars: 1
- Watchers: 3
- Forks: 3
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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# 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](https://hub.docker.com/u/hbpmip/dashboard/).
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](mip-base/r-mip/README.md) 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](https://docs.docker.com/engine/installation/ubuntulinux/) and [captain](https://github.com/harbur/captain).
If you are working on the MIP, please use the [dev setup](https://github.com/LREN-CHUV/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).