RunRAxMLdna: RAxML

Description

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

Usage

RunRAxMLdna(user.name, token, DE.file.name = "", DE.file.path =
                 "", job.name = NULL, model = "GTRCAT", bootstrap =
                 NULL, algorithm = "d", multipleModelFileName = NULL,
                 numcat = 25, nprocs = 2, version =
                 "raxml-lonestar-7.2.8u1")

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 GTRCAT, GTRGAMMA, GTRCAT.GAMMA, GTRGAMMAI, GTRCAT.GAMMAI

bootstrap

Random Seed Number for non-parametric bootstrapping

algorithm

Select the type of algorithm/function you want. "d" is default.

multipleModelFileName

substitution model file

numcat

Number of distinct rate categories

nprocs

the number of processors to be allocated to the job, default = 2

version

RAxML version, options include raxml-lonestar-7.2.8u1

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.

Examples

Run this code

# RunRAxMLdna(user.name, token, DE.file.name="ex.lp.fasta", model="GTRCAT",
	#              bootstrap=NULL, numcat=25)