thibautjombart / adegenet_docker

Docker images for the R package adegenet

adegenet docker images

What is this?

Docker provides a robust, lightweight way to ship applications within a small, self-sufficient operating system, which includes all the dependencies and tools required for the app the run smoothly. This structure is called a container, and different versions of a container are referred to as images.

adegenet docker images are meant first for testing, but can also be used for data analysis.

How can I use it?

Installing docker

First of all, you need docker installed on your computer. Follow this link for guidelines to install Docker Community Edition.

Then you need to choose the adegenet docker image you want to use (see next sections on available images), and choose how you want to use the image. There are two recommended ways to use adegenet docker images: starting a Rstudio server, or starting a bash session.

adegenet_server with a Rstudio session

This approach is aimed at regular users, and is meant to be used with the adegenet_server image. This image is used to start a Rstudio server, which enable the user to start a Rstudio session within a web browser, with the devel version of adegenet and its dependencies pre-installed.

You can download / update the image by typing:

docker pull thibautjombart/adegenet_server

Then, to start image and use it to launch a local Rstudio server:

docker run -d -p 8787:8787 thibautjombart/adegenet_server

A Rstudio session can then be started by opening a web browser and going to the URL 127.0.0.1:8787 (or localhost:8787). The login and password are 'rstudio'. Also note that the port (8787) can be changed if necessary.

adegenet_testing and a bash session

This approach is recommended for developers, and is especially useful for testing. It is meant to be used with the adegenet_testing image. It will open a bash shell logged as guest within the /home/guest. A folder /home/guest/dev will contain git clones of the various installed packages. A R session can be started (without support for graphics) simply by typing R.

You can download / update the image by typing:

docker pull thibautjombart/adegenet_testing

To start the docker image with a bash shell, type:

docker run --rm -it --user guest thibautjombart/adegenet_testing /bin/bash

Building the docker image

Both images are kept up-to-date with adegenet devel automatically (any push to the github repository of adegenet triggers a new build). The example below is for building images locally, which can be useful to develop your own images based on the adegenet ones.

This is an example building the adegenet_testing image, but the same can be applied to other images. Replace thibautjombart wherever appropriate by your docker account. To build the image, you first need to download the Dockerfile (docker/testing/Dockerfile), and then type (from the folder where Dockerfile is present):

docker build -t adegenet_testing .

To tag the image, then use:

docker tag adegenet_testing thibautjombart/adegenet_testing:latest

To publish the image:

docker push thibautjombart/adegenet_testing:latest