Installing R packages on the HPC (Not Needed Today)
Just like R Studio on a Windows Computer, before you can run your R script you need to install the packages your script needs. We have done this for you for this training session but to install your own packages you can follow a procedure like this:
bioconductor_packages <- c("clusterProfiler", "pathview", "AnnotationHub", "org.Hs.eg.db")
cran_packages <- c("tidyverse", "ggplot2", "plyr", "readxl", "scales")
# Compares installed packages to above packages and returns a vector of missing packages
new_packages <- bioconductor_packages[!(bioconductor_packages %in% installed.packages()[,"Package"])]
new_cran_packages <- cran_packages[!(cran_packages %in% installed.packages()[,"Package"])]
# Install missing bioconductor packages
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(new_packages)
# Install missing cran packages
if (length(new_cran_packages)) install.packages(new_cran_packages, repos = "http://cran.us.r-project.org")
# Update all installed packages to the latest version
update.packages(bioconductor_packages, ask = FALSE)
update.packages(cran_packages, ask = FALSE, repos = "http://cran.us.r-project.org")
Save this as install.R
You can then run this on the HPC like before with this submission script:
#!/bin/bash -l #PBS -N R_install #PBS -l select=1:ncpus=1:mem=4gb #PBS -l walltime=2:00:00 #PBS -m abe module load r/4.2.1-foss-2022a cd $PBS_O_WORKDIR Rscript install.R
Save this as install.pbs
Run this on the HPC:
# Submit the job to the HPC qsub install.pbs # Check the status of the job qjobs