Add a Dockerfile to build docker images

[Chris-Schnaufer]

Building Docker images with the base requirements met would allow others to use FIELDimageR with less startup overhead.

I created a Dockerfile at https://github.com/Chris-Schnaufer/FIELDimageR/blob/add_dockerfile/Dockerfile that can be merged (if desired) and used to build and distribute a Docker image.

[dlebauer]

A few thoughts:

• Use a versioned image?
• rocker provides scripts install2.r and installGithub.r that simplifies installation of R packages. So an alternative for installing the R packages might be:

FROM rocker/rstudio:3.6.3
MAINTAINER="Chris Schnaufer <schnaufer@email.arizona.edu>"

RUN apt-get update && apt-get install -y --no-install-recommends \
    libxml2-dev 
    zlib1g-dev 
    libfftw3-dev 
    gdal-bin 
    libgdal-dev 
    libxt-dev

RUN install2.r --error \
    sp
    raster
    rgdal
    scales
    xml2
    git2r
    usethis
    fftwtools
    devtools

RUN installGithub.r filipematias23/FIELDimageR

In addition, If you start from rocker/geospatial you get a lot of these dependencies already built in (including tidyverse and a lot of geospatial utilities - not just those required by FieldImageR but some that could be useful for running downstream analyses, as well as a lot of bloat!!)

• it is quite a stack (not clear if additional size / dependencies are worth it), but
  • rocker/geospatial https://github.com/rocker-org/geospatial/blob/master/Dockerfile builds on
  • rocker/verse https://github.com/rocker-org/rocker-versioned/blob/master/verse/3.6.3.Dockerfile which builds on
  • rocker/tidyverse https://github.com/rocker-org/rocker-versioned/blob/master/tidyverse/3.6.3.Dockerfile which builds on
  • rocker/rstudio https://github.com/rocker-org/rocker-versioned/blob/master/rstudio/3.6.3.Dockerfile which builds on
  • rocker/r-ver which is the base for the versioned images ...

[filipematias23]

Thank you for sharing ..!!!

[Chris-Schnaufer]

I have updated the Dockerfile to take advantage of suggested installation changes.

I am putting the suggested additions for downstream analysis into another issue: #9

[Chris-Schnaufer]

Linking to #10

[dlebauer]

this can be closed since #10 has been merged and suggestions for improvement are in #9

[filipematias23]

Hi @Chris-Schnaufer and @dlebauer,
Thank you a lot for helping with this project.
I am wondering what is the next step? How can I integrate your suggestions (#9 and #10) to the tutorial?

All the best,
Filipe

[Chris-Schnaufer]

I am wondering what is the next step? How can I integrate your suggestions (#9 and #10) to the tutorial?

I think the next step as described in #9 would be to determine if those are changes that are desired and, if so, update the Dockerfile to use the new base image. I don't know who would be best suited to determine if those changes are desired