rpackages.R

Sys.setenv(TAR = "/bin/tar")
options(repos=structure(c(CRAN="https://cloud.r-project.org")))

if (!requireNamespace('BiocManager', quietly = TRUE)) {
    install.packages('BiocManager')
    BiocManager::install("remotes")
}

args <- commandArgs(trailingOnly=TRUE)
packages <- read.csv(args[1], stringsAsFactors = FALSE,
                     header = TRUE, sep = " ", comment.char = "#")
installed <- rownames(installed.packages())
for (i in 1:nrow(packages)) {

    pckg_name = tail(unlist(strsplit(packages[i,1], split = "/")), n = 1)

    if (pckg_name %in% installed) {
        message(paste(pckg_name, "already installed"))
    } else {
        if (packages[i,2] == TRUE) {
            INSTALL <- BiocManager::install
        } else {
            INSTALL <- install.packages
        }
        package <- packages[i,1]
        message(paste("install", package))
        INSTALL(packages[i,1])
        message(paste("installed", package))
    }
}


#library(devtools)
#install_github("immunogenomics/harmony")
#install_github("theislab/kBET")