rPlant (version 1.2)

RunRAxMLprotein: RAxML

Description

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

Usage

RunRAxMLprotein(user.name, token, DE.file.name="", DE.file.path="", job.name=NULL, model="PROTCAT", bootstrap=NULL, numcat=25, nprocs=1)

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

model

Substitution model. Choices are PROTCAT, PROTGAMMA, PROTCAT.GAMMA, PROTGAMMAI, PROTCAT.GAMMAI

bootstrap

Random Seed Number for non-parametric bootstrapping

numcat

Number of distinct rate categories

nprocs

the number of processors to be allocated to the job, default = 1

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

# RunRAxMLprotein(user.name, token, DE.file.name="your.protein.alignment", DE.file.path="",  model="PROTCAT.GAMMA", bootstrap=NULL, numcat=25, nprocs=1)