Install and run R package grantfigs201710 on SLURM cluster

sense-pat.sh

#!/bin/bash
#SBATCH -o sense-pat.out

set -e

# Globals
repo="grantfigs201710"

main() {
    test -n "$SLURM_JOB_ID" && echo "Job $SLURM_JOB_ID" >> sense-pat.out
    module purge
    bootstrap
    update
    run
}

# Install R and Bioconductor installer.
bootstrap() {
    conda install -y -c r r-essentials r-xml r-devtools
    Rscript -e 'source("https://bioconductor.org/biocLite.R")'
}

# Update our package.
update() {
    local github git
    github="CoreLab/$repo"

    module load git
    if ! [[ -d "$repo" ]]; then
        git clone git@github.uconn.edu:${github}.git
    fi
    (
	# Old versions of git do not support --git-dir=$repo/.git
	# --work-tree=$repo
	cd $repo
	git pull
	R -q --vanilla <<EOF
devtools::install(
    dependencies = c("Imports", "Suggests"),
    repos = BiocInstaller::biocinstallRepos())
EOF
    )
}

# Run vignette.
run() {
    R -q --vanilla <<EOF
setwd("$repo/vignettes")
library(BiocParallel)
register(MulticoreParam($SLURM_JOB_CPUS_PER_NODE))
devtools::build_vignettes()
EOF
}

main