nicoinn / dada2docker

Docker build instructions for DADA2 and related functionality

Docker DADA2

This repo contains docker build instructions for images:

• base -- release version of dada2 -- joey711/dada2-base
• base-devel -- development version of dada2 -- joey711/dada2-base-devel
• rstudio-devel -- RStudio Server image with devel dada2 -- joey711/dada2-rstudio-devel
• shiny-devel -- Shiny-dada2 app pre-installed on Shiny-Server image -- joey711/dada2-shiny-devel

Quick Start

1. Install Docker if you haven't already.
2. docker run <DockerParams> joey711/dada2-<ImageName>
3. When done: do CTL-C at the terminal, or docker container kill <container name>. docker container ls will show you the container name.

Shiny-rstudio

To host RStudio Server with dada2-devel pre-installed

docker run -d -p 8787:8787 -v ~:/home/rstudio/ joey711/dada2-rstudio-devel

• Where ~ can be replaced by a local (host) directory of your choice.
• You can also add -v args for making additional folders available in your Rstudio session.
• Point a browser window to 0.0.0.0:8787 while the container is running to start working in RStudio.

Shiny-dada2

The run invocation has the following pattern (see the included runshinydada2.sh file for additional tips):

docker run --rm -p 3838:3838 \
    -v ~/Downloads/:/home/rstudio/Downloads/ \
    joey711/dada2-shiny-devel

• Where ~/Downloads/ should be replaced by a data directory on your machine that you want to "explore" with Shiny-dada2.
• Point a browser window to 0.0.0.0:3838 while the container is running.