Install Seurat easily and effectively

install_seurat.R

#!/usr/bin/env Rscript

args <- commandArgs(trailingOnly = TRUE)

msg <- "Please pass 'bitbucket' or 'github' to choose where we install Seurat from"

if (length(x = args) != 1) {
    stop(msg)
}

library.path <- '~/R/packages'
seurat.bitbucket <- 'nygcresearch/seurat'
# seurat.bitbucket <- '[email protected]:nygcresearch/seurat.git'
seurat.github <- 'satijalab/seurat'

# A list of packages from CRAN

cran.packages <- c(
    'devtools',
    'getPass',
    'enrichR'
)

# A list of packages from BioConductor

bioc.packages <- c(
    'AnnotationDbi',
    'impute',
    'GO.db',
    'preprocessCore',
    'made4'
)

#   Functions to install dependencies
#   BioConductor dependencies
BioCInstall <- function(package.list) {
    ifelse(
        test = 'biocLite' %in% rownames(x = installed.packages()),
        yes = print('Found biocLite'),
        no = source(file = "http://bioconductor.org/biocLite.R")
    )
    # library(BiocInstaller)
    for (package in package.list) {
        ifelse(
            test = package %in% rownames(x = installed.packages()),
            yes = print(paste('Found', package)),
            no = BiocInstaller::biocLite(package)
        )
    }
}

#   Cran dependencies
InstallCRANPackage <- function(package) {
    tryCatch(
        expr = ifelse(
            test = package %in% rownames(x = utils::installed.packages()),
            yes = print(paste('Found', package)),
            no = install.packages(package)
        ),
        error = function(e) {cat()}
    )
}

#   Set library path
.libPaths(new = library.path)

#   Set CRAN mirror
options(repos = c(CRAN = "https://cran.rstudio.com"))

#   Install BioConductor packages
BioCInstall(package.list = bioc.packages)

#   Install CRAN packages
for (package in cran.packages) {
    if (nchar(x = package) >= 1) {
        InstallCRANPackage(package = package)
    }
}

#   Install Seurat
seurat.source <- tolower(x = args[1])
if (seurat.source == 'github') {
    devtools::install_github(repo = seurat.github)
} else if (seurat.source == 'bitbucket') {
    cat("Be sure to use an account with admin access\n")
    cat("Seurat branch (eg 'master'): ")
    branch <- readLines(con = 'stdin', n = 1)
    # cat(branch, '\n')
    cat("Bitbucket username: ")
    user <- readLines(con = 'stdin', n = 1)
    # cat(user, '\n')
    passwd <- getPass::getPass(msg = 'Bitbucket password: ')
    devtools::install_bitbucket(
        repo = seurat.bitbucket,
        ref = branch,
        auth_user = user,
        password = passwd
    )
} else {
    stop(msg)
}