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.path="", DE.file.list,
          input.list, job.name, nprocs=1, args=NULL, print.curl=FALSE)
CheckJobStatus(user.name, token, job.id, verbose=FALSE, print.curl=FALSE)
DeleteJob(user.name, token, job.id, print.curl=FALSE)
RetrieveJob(user.name, token, job.id, files, zip, print.curl=FALSE)
ListJobOutput(user.name, token, job.id, print.curl=FALSE)
GetJobHistory(user.name, token, verbose=FALSE, print.curl=FALSE)

Arguments

user.name

iPlant Discovery Environment user name

token

A validation tool used in place of unencrypted passwords

application

Name of DE application

DE.file.path

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

DE.file.list

A list of input files, many functions only have one input file, but some have multiple input files, in that case input all those files in list form. This list is the same length as input.list, and input.list[[1]] corresponds with DE.file.list[[1]]. See

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

input.list

A list of the name of inputs. See details for more information.

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

print.curl

Prints the Curl Statement that can be used in the terminal

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. For input.list use the GetAppInfo function, the 'kind' column verifies if "input" or "output". What goes in the input.list is only the name in the 'id' column when the 'kind' column is "input". For example, when the application is "muscle-lonestar-3.8.31u2", from the GetAppInfo(user.name, token, "muscle-lonestar-3.8.31u2")[[2]], we get the input.list=list("stdin"). For the application "velveth-1.2.07u1", again using GetAppInfo(user.name, token, "velveth-1.2.07u1")[[2]], the input.list=list("reads1", "reads2", "reads3", "reads4", "reads5", "reads6"). A couple notes, the input.list can be shorter than the the number of inputs, for example, using the "velveth-1.2.07u1" application, the input list could be input.list=list("reads1", "reads2", "reads3"). Also, the DE.file.list is the same length as input.list, and in this example, lets say DE.file.list=list("filer", "filea", "filez"), then "filer" corresponds with the "read1" input.

Examples

Run this code

# 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-lonestar-3.8.31u2",
#                    DE.file.list=list("ex.lp.fasta"), input.list=list("stdin")
#                    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)