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

In tgirke/systemPipeR: systemPipeR: workflow management and report generation environment

Interface to allow full use of the Environment Modules system for Unix

Description

The function module enables use of the Environment Modules system (http://modules.sourceforge.net/) from within the R environment. The user's login shell environment (i.e. 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

module(action_type, module_name = NULL)
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. Examples: "hisat2", "hisat2/2.1.0", c("hisat2", "samtools").

Details

Partial failure would also result 'FALSE', e.g. "load" two modules, one successful and the other failed, then the return is 'FALSE'. For "unload" action will always return 'TRUE' even if the module is not loaded at all or not found.

Author(s)

Tyler Backman, Jordan Hayes and Thomas Girke

Examples

## 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("hisat2/2.2.1")

## 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 March 27, 2024, 11:31 p.m.