Develop Bioconductor packages with docker container

Aug 6, 2019 2 min read R, bioinformatics, package

Readings

links to read:

I am following the last link.

pull the container

docker pull bioconductor/bioconductor_full:devel
docker images 

REPOSITORY                       TAG                  IMAGE ID            CREATED             SIZE
bioconductor/bioconductor_full   devel                ae3ec2be7376        3 hours ago         5.7GB
seuratv3                         latest               9b358ab1fd63        2 days ago          2.76GB

It is 5.7G in size.

start the Rstuido from the image. I have another Rstudio instance using port 8787, let me use a different one (e.g. 8080). docker Rstudio default port is 8787, change the host port to 8080.

mkdir -p ~/R/host-site-library

docker run                                      \
  -e PASSWORD="xyz"                   \
  -p 8080:8787                                \
  -v ~/R/host-site-library:/usr/local/lib/R/host-site-library  \
  -v ~/github_repos:/home/rstudio \
  bioconductor/bioconductor_full:devel

NOTE: The path ~/R/host-site-library is mapped to .libPaths() in R. So, when R is started, all the libraries in the host directory host-site-library are available to R. It is stored on your machine mounted from the volume you fill in place of host-site-library.

The mounted path must be an absolute path.

I also mounted the github_repo folder in my host machine to the docker home directory. Because every time you exit a container and start it again, the modification you did to the container will be gone (unless you make an modified image and use that for the next time). I will save the R package in my ~/github_repo folder in the host machine.

type localhost:8080, you should see the Rstudio login page. username is rstudio, password is xyz in this dummy example.

In Rstudio:

> .libPaths()
[1] "/usr/local/lib/R/host-site-library" "/usr/local/lib/R/site-library"     
[3] "/usr/local/lib/R/library"

you will see /usr/local/lib/R/host-site-library is in the libpath, that corresponds to the ~/R/host-site-library in the host machine, if you do package installation, it will be installed in the~/R/host-site-library .

start an R package use usethis

follow these two blog posts and R packages book by Hadley Wickham:

install.packages(c("devtools", "roxygen2", "usethis", "available", "rmarkdown"))

## check if the package name is avaiable (not used by others)
library(available)
available("myawesomepackage")

library(usethis)
usethis::create_package("~/myawesomepackage")

use_git()
use_github()
use_mit_license("Ming Tang")
usethis::use_pipe()

Add a function

usethis::use_r("myawesomefunc")

On mac:
command + option + shift + R for inserting roxygen comment.
command + shift + D for documentation.
command + shfit + B for building package.

add more functions, repeat.

Next is to add test and setup some continuous integration. Read this Automate testing of your R package using Travis CI, Codecov, and testthat by Jean Fan.

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