RLinuxModules

R package that makes linux environment modules available from R.

Note: Lmod environment module system have support for R so this package is not needed.

installation

devtools::install_github("larsgr/RLinuxModules")

use example:

library(RLinuxModules)

moduleInit( modulesHome = "yourpathToModulesEnvironment")

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

system("samtools") # samtools should now be available (if you have that module)

How it works

The Modules Environment does not support R scripting but does support Python. 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