transgirlcodes / dockerized_hybridcheck

A Docker container of the R package HybridCheck and all of it's dependencies.

Dockerized HybridCheck R package

This is the Dockerized R bundled with the R package HybridCheck and its dependencies.

The image is available from Docker Hub.

Usage:

Basic use:

To use this container you will need Docker installed on your computer.

To run R with HybridCheck on your computer in a terminal:

docker run -it ward9250/hybridcheck

Mounting directories with data:

You will probably want to mount your current working directory (i.e. the one with the data files you want to analyze with HybridCheck) so as the Docker container can 'see' the directory and your files.

docker run -ti --rm -v "$PWD":/home/docker/mydatafiles -w /home/docker/mydatafiles -u docker r-base

Running your analysis using your own Dockerfile:

As an alternative to the command for running the Docker container with a mounted working directory (above), you can collect the scripts and data needed to run your analysis, into a folder with your own Dockerfile for your analysis/project. The Dockerfile you put in this directory should specify ward9250/hybridcheck in the FROM line. An example Dockerfile which does this is below:

FROM ward9250/hybridcheck:latest
COPY . /home/docker/myanalysis
WORKDIR /home/docker/myanalysis
CMD ["Rscript", "myscript.R"]

Once you have made your Dockerfile and have it in the directory along with your R script and data-files, you can build it and then run your analysis, by executing the following command from your projects folder:

docker build -t myproject .

Then you can run the Docker container of your analysis you just built:

docker run myproject

Intended purpose:

This container was created to avoid issues installing and running the R package 'HybridCheck'. Common issues installing and running these include different versions of R or R packages, non-standard R library locations and so on.

If you learn Docker enough to use it to download and run containers, you avoid all these possible pitfalls, as everything needed to get the package running is provided for in this container, which will run on any system Docker is available for, which certainly covers Windows, OS X, and the popular GNU/Linux distros.