warrenson/rlinuxmodules

R package that makes linux environment modules available from R

RLinuxModules

R package that makes linux environment modules available from R.

Installation

You can install the released version of RLinuxModules from CRAN with:

# Not released to CRAN
# install.packages("RLinuxModules")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("kiwiroy/RLinuxModules@main")

Example

This is a basic example which shows you how to solve a common problem when using environment modules with R:

library(RLinuxModules)

# initialise
moduleInit(modulesHome = modulesHome)

# load samtools into the environment
module("load samtools") 

# samtools should now be available
system("samtools", intern = TRUE)

While in a knitr code chunk using bash as the engine.

# Environment is inherited in other code chunks.
which samtools

# see known issues below
module list

How it works

The Modules Environment now supports R scripting since version 4.0. This package works by using the python support and translating the python commands returned from modulecmd python into R commands. It has only been tested for version 3.2.10

Known issues

1. If /bin/sh is symlinked to /bin/dash, dash will sanitize the environment in such a way that the module function is not available to the child bash shell. See a bug report and Stack Overflow question on the topic.