module: Linux Environment Modules interface

Description Usage Arguments Details Value Examples

View source: R/module.R

Description

Access the linux Environment Modules which provides for the dynamic modification of a user's environment via modulefiles.

Usage

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module(Arguments)

Arguments

Arguments

"[ switches ] [ subcommand ] [ subcommand-args ]" See examples.

Details

Each modulefile contains the information needed to configure the shell for an application. Once the RLinuxModules package is initialized (with moduleInit), the environment can be modified on a per-module basis using the module command which interprets modulefiles. Typically modulefiles instruct the module command to alter or set shell environment variables such as PATH, MANPATH, etc. modulefiles may be shared by many users on a system and users may have their own collection to supplement or replace the shared modulefiles.

Value

Output messages will be sent to stderr

Examples

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module("avail") # shows available modules

module("--help") # show available sub-commands and switches

module("load samtools") # loads the module "samtools"
system("which samtools") # check that samtools is loaded in the environment

module("list") # list loaded modules

module("unload samtools") # unload the samtools module

module("load samtools/1.0") # loads a specific version of the module "samtools"
system("which samtools") # check that the correct samtools is loaded in the environment

larsgr/RLinuxModules documentation built on May 21, 2017, 8:33 a.m.