vimalkvn/dada2 repository overview

⁠A docker image for dada2

This repository contains the Dockerfile for building a Docker⁠ image for dada2⁠ 1.4.0 - an R package for "Fast, accurate, single-nucleotide resolution for amplicon data". You can pull this image using

docker pull vimalkvn/dada2

⁠Notes

1. The docker image built using this Dockerfile will have the DADA2 1.4.0 from BioConductor.

2. R 3.4.0 is used as a base (r-base:3.4.0).

3. To run this container, download the run-dada2⁠ wrapper script available from the Github repository, save it in a location accessible in PATH, make it executable and run it like this:

    run-dada2 script.R
   

   Copy

   or run the container directly like this:

    docker run --rm \
    -e LOGNAME=$(logname) \
    -e USER=$(logname) \
    -u ${UID}:${UID} \
    -v $(pwd):/wdir \
    -w /wdir \
    vimalkvn/dada2 \
    script.R
   

   Copy

   The -e and -u options are used so that the container has permissions to read input files and the generated output files will be owned by the user running the container and not root.

   If you are using one of the methods above, input files are assumed to be present in the directory where the command is run.

   User must have either:

   • sudo access to run this script (script should be run as sudo run-dada2) or the

   • user must be part of the docker user group.

4. This container simply runs Rscript by default and a script can be provided as the first argument. If a command other than Rscript is required, it can be specified using the --entrypoint docker argument.