eDNA docker

This repository contains a Dockerfile used to build the edna_tools docker image including Rstudio web interface and the following packages:

• tidyverse
• dada2
• ggplot
• OBITools
• cutadapt
• MKBRD
• vsearch
• ecoprimers

This docker image allows to run a container with all the software needed for eDNA analysis. Independently from your operating system, ubuntu is launched with all the software pre-installed in a self-contained environment.

Keep in mind that any modifications made inside the container (e.g. packages newly installed or files modified) will be lost after stopping it. Therefore, you need to use the -v argument to mount the local files inside the container as explained in the tutorial bellow. Modification made to the mounted files will not be lost and you can even create new files from inside the container in the mounted path.

The Rstudio web interface provides an R IDE (Integrated Development Environment) in addition to a terminal to execute any bash command you may need.

Docker tutorial

Linux

Start the docker daemon by running:

sudo dockerd

In another terminal, download the image from dockerhub and run it with the following command:

docker run -v path/to/your/local/file:path/inside/the/container -p 8787:8787 thesanc/edna_tools

You should now be able to have access to the Rstudio instance by typing localhost:8787 in your browser. You can log in with rstudio as username and the password provided by the output of the docker run command.

Mac

Windows