rPlant (version 1.2)

SubmitJob: Executing analytical applications

Description

Functions for executing and managing analytical applications deployed in the iPlant infrastructure

Usage

SubmitJob(user.name, token, application, DE.file.name, DE.file.path="", job.name, nprocs=1, args=c())
CheckJobStatus(user.name, token, job.id, verbose=FALSE)
DeleteJob(user.name, token, job.id)
RetrieveJob(user.name, token, job.id, files, zip)
ListJobOutput(user.name, token, job.id)
GetJobHistory(user.name, token, verbose=FALSE)

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).

application

Name of DE application

job.name

The name to give the job being submitted

nprocs

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

args

Optional for arguments (i.e. flags)

job.id

The unique ID number given to a submitted job

DE.file.path

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

verbose

Optional screen output that displays all of the results from the api, default = FALSE

files

Names of output files to download, can be one or many

zip

Zip job files together, default is TRUE

Value

• A job ID is provided for jobs submitted via job.submit.

Details

Application must match an application name directly out of the DE, to ensure, you can check using ListApps. The job.id is returned after submitting, and it is used to check the status or download results. It can also be retrieved using GetJobHistory.

See Also

ListApps

Examples

# Upload a file to the DE
# UploadFile("User", token, local.file.name="ex.lp.fasta", file.type="FASTA-0")

# Submit a MUSCLE job using landplant data, which will return a job.id
# myJob <- SubmitJob("User", application="muscle-ranger-2.0", DE.file.name="ex.lp.fasta", DE.file.path="/data/", job.name="MUSCLE", nprocs="1")

# Check the status of any job
# CheckJobStatus("User", token, myJob, verbose=F)
             
# Lists and output files a job has created
# ListJobOutput("User", token, myJob)  
             
# Download output files
# RetrieveJob("User", token, myJob, ListJobOutput("User", token, myJob)[[1]])
     
# View job history
# GetJobHistory("User", token, verbose=FALSE)

# Delete Job
# DeleteJob("User", token, myJob)