rPlant (version 2.7)

RunClustal: ClustalW alignment

Description

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

Usage

RunClustal(user.name, token, DE.file.name, DE.file.path="", job.name=NULL,
                   nprocs=1,version="ClustalW2-2.1u1")

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

nprocs

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

version

ClustalW version, options include ClustalW2-2.1u1, clustalw2Dispatcher-1.0.13100u1, clustalw2-lonestar-2.1u2

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 to submit ClustalW alignment jobs through the iPlant api.

See Also

SubmitJob

Examples

# RunClustal(user.name, token, DE.file.name="ex.lp.fasta", job.name
	#            ="clustalw.Job1", version="clustalw2-lonestar-2.1u2")