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

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.

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

Tyler Backman, Jordan Hayes and Thomas Girke

Examples