Getting started with dockerfiler

Colin Fay

2022-07-04

dockerfiler

Easy Dockerfile Creation from R.

Installation

You can install dockerfiler from GitHub with:

# install.packages("remotes")
remotes::install_github("colinfay/dockerfiler")

Or from CRAN with :

install.packages("dockerfiler")

Basic worflow

By default, Dockerfiles are created with FROM "rocker/r-base".

You can set another FROM in new()

library(dockerfiler)
# Create a dockerfile template
my_dock <- Dockerfile$new()
my_dock$MAINTAINER("Colin FAY", "contact@colinfay.me")

Wrap your raw R Code inside the r() function to turn it into a bash command with R -e.

my_dock$RUN(r(install.packages("attempt", repo = "http://cran.irsn.fr/")))

Classical Docker stuffs:

my_dock$RUN("mkdir /usr/scripts")
my_dock$RUN("cd /usr/scripts")
my_dock$COPY("plumberfile.R", "/usr/scripts/plumber.R")
my_dock$COPY("torun.R", "/usr/scripts/torun.R")
my_dock$EXPOSE(8000)
my_dock$CMD("Rscript /usr/scripts/torun.R ")

See your Dockerfile :

my_dock
#> FROM rocker/r-base
#> MAINTAINER Colin FAY <contact@colinfay.me>
#> RUN R -e 'install.packages("attempt", repo = "http://cran.irsn.fr/")'
#> RUN mkdir /usr/scripts
#> RUN cd /usr/scripts
#> COPY plumberfile.R /usr/scripts/plumber.R
#> COPY torun.R /usr/scripts/torun.R
#> EXPOSE 8000
#> CMD Rscript /usr/scripts/torun.R

If you’ve made a mistake in your script, you can switch lines with the switch_cmd method. This function takes as arguments the positions of the two cmd you want to switch :

# Switch line 8 and 7
my_dock$switch_cmd(8, 7)
my_dock
#> FROM rocker/r-base
#> MAINTAINER Colin FAY <contact@colinfay.me>
#> RUN R -e 'install.packages("attempt", repo = "http://cran.irsn.fr/")'
#> RUN mkdir /usr/scripts
#> RUN cd /usr/scripts
#> COPY plumberfile.R /usr/scripts/plumber.R
#> EXPOSE 8000
#> COPY torun.R /usr/scripts/torun.R
#> CMD Rscript /usr/scripts/torun.R

You can also remove a cmd with remove_cmd:

my_dock$remove_cmd(8)
my_dock
#> FROM rocker/r-base
#> MAINTAINER Colin FAY <contact@colinfay.me>
#> RUN R -e 'install.packages("attempt", repo = "http://cran.irsn.fr/")'
#> RUN mkdir /usr/scripts
#> RUN cd /usr/scripts
#> COPY plumberfile.R /usr/scripts/plumber.R
#> EXPOSE 8000
#> CMD Rscript /usr/scripts/torun.R

This also works with a vector:

my_dock$remove_cmd(5:7)
my_dock
#> FROM rocker/r-base
#> MAINTAINER Colin FAY <contact@colinfay.me>
#> RUN R -e 'install.packages("attempt", repo = "http://cran.irsn.fr/")'
#> RUN mkdir /usr/scripts
#> CMD Rscript /usr/scripts/torun.R

add_after add a command after a given line.

my_dock$add_after(
  cmd = "RUN R -e 'remotes::install_cran(\"rlang\")'", 
  after = 3
)

Save your Dockerfile:

my_dock$write()

Create a Dockerfile from a DESCRIPTION

You can use a DESCRIPTION file to create a Dockerfile that installs the dependencies and the package.

my_dock <- dock_from_desc("DESCRIPTION")

my_dock$CMD(r(library(dockerfiler)))

my_dock$add_after(
  cmd = "RUN R -e 'remotes::install_cran(\"rlang\")'", 
  after = 3
)