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Last pushed: 4 months ago
Short Description
An image for dada2 R package - http://benjjneb.github.io/dada2/
Full Description

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
    

    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
    

    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.

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vimalkvn
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