Jobs.submitShellCommandJob {SciServer}R Documentation

Submit shell command job

Description

Submits a shell command for execution (as an asynchronous job) inside a Docker compute domain.

Usage

Jobs.submitShellCommandJob(shellCommand, dockerComputeDomain = NULL, dockerImageName = NULL, userVolumes = NULL, dataVolumes = NULL, resultsFolderPath = "", jobAlias = "")

Arguments

shellCommand

shell command (string) defined by the user.

dockerComputeDomain

object (list) that defines a Docker compute domain. A list of these kind of objects available to the user is returned by the function Jobs.getDockerComputeDomains().

dockerImageName

name (string) of the Docker image for executing the notebook. E.g., dockerImageName="Python (astro)". An array of available Docker images is defined as the 'images' property in the dockerComputeDomain object.

userVolumes

a list with the names of user volumes (with optional write permissions) that will be mounted to the docker Image. E.g.: userVolumes = list( list(name="JobsTestVolume", rootVolumeName="Storage", owner="myUserName", needsWriteAccess=TRUE), list(name="scratch", rootVolumeName="Temporary", owner="myUserName", needsWriteAccess=TRUE) ). A list of available user volumes can be found as the 'userVolumes' property in the dockerComputeDomain object. If userVolumes=Null, then all available user volumes are mounted, with 'needsWriteAccess' = TRUE if the user has Write permissions on the volume.

dataVolumes

a list with the names of data volumes that will be mounted to the docker Image. E.g.: dataVolumes=list(list(name='SDSS DAS')). A list of available data volumes can be found as the 'volumes' property in the dockerComputeDomain list. If dataVolumes=NULL, then all available data volumes are mounted.

resultsFolderPath

full path to results folder (string) where the original notebook is copied to and executed. E.g.: /home/idies/workspace/rootVolume/username/userVolume/jobsFolder. If not set, then a default folder will be set automatically.

jobAlias

alias (string) of job, defined by the user.

Value

the job ID (integer)

Author(s)

Manuchehr Taghizadeh-Popp
Maintainer: Manuchehr Taghizadeh-Popp <mtaghiza@jhu.edu>

References

http://www.sciserver.org
http://apps.sciserver.org
http://www.github.com/sciserver/SciScript-R

See Also

Jobs.submitNotebookJob,Jobs.getJobStatus,Jobs.getDockerComputeDomains,Jobs.cancelJob

Examples

jobId = Jobs.submitShellCommandJob("pwd")

[Package SciServer version 2.0.0 Index]