rPlant (version 1.2)

RunMuscle: MUSCLE alignment

Description

This function will submit a MUSCLE job to iPlant's DE

Usage

RunMuscle(user.name, token, DE.file.name="", DE.file.path="", job.name=NULL, version="muscle-ranger-2.0")

Arguments

user.name

iPlant Discovery Environment user name

token

a validation tool used in place of unencrypted passwords

DE.file.name

name of file to be evaluated on the Discovery Environment (DE).

DE.file.path

optional path to a user's subdirectory on the DE; default path is empty, which leads to the home directory

job.name

the name to give the job being submitted

version

MUSCLE version, options include muscle-ranger-2.0, Muscle-3.8.31, muscle-lonestar-3.8.31, and muscle-ranger1.3-1.3

Value

• Text listing action as either being a "success" or "error". If an error, then a message stating the error should also be reported.

Details

The function is a wrapper function for several other rPlant functions, but specific to MUSCLE runs.

See Also

SubmitJob

Examples

# RunMuscle(user.name, token, DE.file.name="ex.lp.fasta", job.name="muscleJob1", DE.file.path="", version="muscle-trestles-2.0")