10-singularity-build-rstudio
Last updated on 2024-03-11 | Edit this page
Estimated time: 35 minutes
Disclaimer
This build of rstudio is for demonstration purposes only on these demo instances. For production purposes please consult your local system admin.
Containerizing Rstudio
CITE ROCKER AND RICHARD
To start, create a few directories Rstudio server looks for.
BASH
workdir=/projects/my-lab/10-build-rstudio
mkdir -p -m 700 ${workdir}/run ${workdir}/tmp ${workdir}/var/lib/rstudio-server
cat > ${workdir}/database.conf <<END
provider=sqlite
directory=/var/lib/rstudio-server
ENDTo start, let’s create an empty file to use as our recipe file. #lets build an Rstudio server and install a few R/Bioconductor pacages into the container.
BASH
Bootstrap: docker
From: rocker/tidyverse:4.2.1
#This def file doesn't seem to build on Sumner with Centos 7. Richard suggests building on an Ubuntu system but we will stick with Centos 7.
%post
apt update
apt install -y libgeos-dev libglpk-dev # libcurl4-openssl-dev
apt install -y libcurl4-gnutls-dev libxml2-dev cmake libbz2-dev
apt install -y libxslt1-dev # install for sandpaper
R -e 'if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")'View files inside directory. Notice no R directory.
Set the run time variables and deploy.
BASH
export SINGULARITY_BIND="${workdir}/run:/run,${workdir}/tmp:/tmp,${workdir}/database.conf:/etc/rstudio/database.conf,${workdir}/var/lib/rstudio-server:/var/lib/rstudio-server"
export SINGULARITYENV_USER=$(id -un)
export SINGULARITYENV_PASSWORD=password
singularity exec --cleanenv rdeseq2.sif rserver --www-port 8787 --auth-none=0 --auth-pam-helper-path=pam-helper --auth-stay-signed-in-days=30 --auth-timeout-minutes=0 --server-user "student"navigate to <your_IP>:8787
username is student password is set above to
password
Lets load a package that from the container.
R
library('DESeq2')
Using the Rstudio file browser look at the R folder that appeared, but nothing is in it.
Lets install something to the user space.
R
BiocManager::install("EnhancedVolcano")
Now we see the local user install.
R
.libPaths()
OUTPUT
[1] "/home/student/R/x86_64-pc-linux-gnu-library/4.2"
[2] "/usr/local/lib/R/site-library"
[3] "/usr/local/lib/R/library" Verify the libs with terminal tabls /home/student/R/x86_64-pc-linux-gnu-library/4.2ls /usr/local/lib/R
Verify via ssh’ing with another tabssh student@<IP>ls /home/student/R/x86_64-pc-linux-gnu-library/4.2
ls /usr/local/lib/R
Lets install few fun packages.
R
install.packages('knitr', dependencies = TRUE)
R
options(repos = c(
carpentries = "https://carpentries.r-universe.dev/",
CRAN = "https://cran.rstudio.com/"
))
install.packages("sandpaper", dep = TRUE)
note the sandpaper command will reset the rstudio
server.
select dont save
R
library('sandpaper')
sandpaper::create_lesson("~/r-intermediate-penguins")
after reset we are now in the new folder
R
sandpaper::serve(quiet = FALSE, host = "0.0.0.0", port = "8789")
Now edit one of the episodes
R
servr::daemon_stop()
Knit example
Make new folder called myknit.
Make file in folder called myknit.Rmd
Copy section of code (lines 56 to 101) from the link below and paste
into new myknit.Rmd file.
#https://github.com/sachsmc/knit-git-markr-guide/blob/master/knitr/knit.Rmd
Caution: just an example below, use copy lines from link above
R
```{r setup, include=FALSE}
library(stringr)
library(knitr)
opts_chunk$set(tidy = FALSE)
knit_hooks$set(source = function(x, options){
if (!is.null(options$verbatim) && options$verbatim){
opts = gsub(",\\s*verbatim\\s*=\\s*TRUE\\s*", "", options$params.src)
bef = sprintf('\n\n ```{r %s}\n', opts, "\n")
stringr::str_c(
bef,
knitr:::indent_block(paste(x, collapse = '\n'), " "),
"\n ```\n"
)
} else {
stringr::str_c("\n\n```", tolower(options$engine), "\n",
paste(x, collapse = '\n'), "\n```\n\n"
)
}
})