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DADA2 Docker image

A simplified, updated repository based on the dada2docker repo from Paul J. McMurdie. This provides an isolated environment from which to run DADA2, a tool for analyzing amplicon sequencing data. If you want to run a version of DADA2 that has system requirements that don't line up with your local environment (DADA2 v1.18 requires R version 3.6.1, for example), running the containerized version may simplify the process. This image also includes the decontam package, and uses Bioconductor v3.12.

Use

By default, the container drops you into an R session. If this is how you intend to use the container, interacting with the R application directly, you'll want to launch the container in "interactive" mode, with the i and t flags:

docker run -it blekhmanlab/dada2

Or, using the Singularity runtime:

singularity run docker://blekhmanlab/dada2

Once the container starts, running library(dada2) will load DADA2, and packageVersion('dada2') should confirm that you have the correct version. Exiting the R application will cause the container to shut down.

Running R scripts

There are a few more steps if you want to run an R script in your container, rather than working interactively in the R shell:

  1. You will need to get your R script into the container. Docker bind mounts enable you to do this; their documentation explains how.
  2. Once you specify a location in the container's filesystem where your R script should live once it starts, you need to specify what command the container should run on startup, rather than just R, which it runs by default.

An example, that assumes you have an R script called test.R in the directory you are currently in on the host machine:

docker run -it -v "$pwd":/cool_demonstration blekhmanlab/dada2 Rscript /cool_demonstration/test.R

This will mount the current working directory on the host machine to a location called /cool_demonstration within the container. So your script will be in the container at /cool_demonstration/test.R, and on startup the container will run the Rscript /cool_demonstration/test.R command and then exit.

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