moduleload: Interface to allow full use of the Environment Modules system...

Description Usage Arguments Author(s) Examples

View source: R/module.R

Description

The function module enables use of the Environment Modules system (http://modules.sourceforge.net/) from within the R environment. By default the user's login shell environment (ie. bash -l) will be used to initialize the current session. The module function can also; load or unload specific software, list all the loaded software within the current session, and list all the applications available for loading from the module system. Lastly, the module function can remove all loaded software from the current session.

Usage

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module(action_type, module_name="")
moduleload(module_name)
moduleUnload(module_name)
modulelist()
moduleAvail()
moduleClear()
moduleInit()

Arguments

action_type

Name of the action to be executed as character vector. The following switches are accepted: avail, list, init, load, unload, and clear.

module_name

Name of software to load as character vector.

Author(s)

Tyler Backman, Jordan Hayes and Thomas Girke

Examples

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## Not run: 
## List all available software from the module system
avail <- moduleAvail()

## List loaded software in the current session
modulelist()

## Example for loading a software into the shell environment
moduleload("hisat2") 
moduleload(modules(args)) 

## Example for removing software from the shell environment
moduleUnload("hisat2")

## Clear all of the software from the shell's initialization files
moduleClear()

## List and load all the software loaded in users default login shell into the current session (default)
moduleInit()

## End(Not run)

tgirke/systemPipeR documentation built on July 20, 2021, 10:45 p.m.