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First, in RStudio create a new R script (File → New File → R script), and save as install.R
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# This line will use the Canberra mirror for CRAN chooseCRANmirror(graphics = getOption("menu.graphics"), ind = 3, local.only = TRUE) # Sometimes you need to install packages from github, like this: install.packages("devtools", repos = "https://cran.csiro.au/")) devtools::install_github("YuLab-SMU/ggtree") # Sometimes you have 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", version = "3.16") BiocManager::install(new_packages, dependencies = TRUE, INSTALL_opts = '--no-lock') # Install missing cran packages if (length(new_cran_packages)) install.packages(new_cran_packages, repos = "https://cran.csiro.au/") # Update all installed packages to the latest version update.packages(bioconductor_packages, ask = FALSE) update.packages(cran_packages, ask = FALSE, repos = "https://cran.csiro.au/") |
Then, in RStudio create a new Text File (File → New File → Text File), and save as install.pbs
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#!/bin/bash -l #PBS -N R_install #PBS -l select=1:ncpus=1:mem=4gb #PBS -l walltime=2:00:00 #PBS -m abe cd $PBS_O_WORKDIR module purge module load r/4.2.2-foss-2022b mkdir -p $PBS_O_WORKDIR/r_library export R_LIBS_USER='$PBS"${PBS_O_WORKDIR}/r_library'" echo $R_LIBS_USER Rscript install.R |
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