Package fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters

Class BpipeTaskScheduler

java.lang.Object

fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler

fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler

fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler

All Implemented Interfaces:

ClusterTaskScheduler, TaskScheduler

Direct Known Subclasses:

BundledScriptBpipeTaskScheduler, DummyTaskScheduler, TGCCTaskScheduler

public abstract class BpipeTaskScheduler
extends AbstractClusterTaskScheduler

This class allow to submit, stop and get the status of jobs using Bpipe scheduler wrappers.

Since:

2.0

Author:

Laurent Jourdren

Nested Class Summary

Nested classes/interfaces inherited from class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler

AbstractClusterTaskScheduler.ProcessThreadOutput

Nested classes/interfaces inherited from interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler

ClusterTaskScheduler.StatusResult, ClusterTaskScheduler.StatusValue

Constructor Summary

Constructors

Constructor	Description
BpipeTaskScheduler()

Method Summary

Modifier and Type	Method	Description
protected Map<String,String>	additionalScriptEnvironment()	Define additional environment variable for bpipe scripts.
void	cleanupJob(String jobId)	Cleanup after a job.
void	configure(Settings settings)	Configure the scheduler.
protected abstract File	getBpipeCommandWrapper()	Get the path to the Bpipe command wrapper.
ClusterTaskScheduler.StatusResult	statusJob(String jobId)	Get the status of a job.
void	stopJob(String jobId)	Stop a job.
String	submitJob(String jobName, List<String> jobCommand, File jobDirectory, int taskId, int requiredMemory, int requiredProcessors)	Submit a job.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler

stop, submit

Methods inherited from class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler

afterExecuteTask, beforeExecuteTask, executeTask, getResult, getStatus, getStep, getStep, getTaskDoneCount, getTaskRunningCount, getTaskSubmittedCount, getTotalTaskDoneCount, getTotalTaskRunningCount, getTotalTaskSubmittedCount, isStarted, isStopped, start, submit, waitEndOfTasks

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler

getSchedulerName

Methods inherited from interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler

getResult, getStatus, getTaskDoneCount, getTaskRunningCount, getTaskSubmittedCount, getTotalTaskDoneCount, getTotalTaskRunningCount, getTotalTaskSubmittedCount, start, submit, waitEndOfTasks

Constructor Detail

BpipeTaskScheduler

public BpipeTaskScheduler()

Method Detail

getBpipeCommandWrapper

protected abstract File getBpipeCommandWrapper()

Get the path to the Bpipe command wrapper.

Returns:

the File object with the path to the Bpipe command wrapper

configure

public void configure(Settings settings)
               throws EoulsanException

Description copied from interface: ClusterTaskScheduler

Configure the scheduler.

Parameters:

settings - Eoulsan settings

Throws:

EoulsanException - if an error occurs while configuring the scheduler

submitJob

public String submitJob(String jobName,
                        List<String> jobCommand,
                        File jobDirectory,
                        int taskId,
                        int requiredMemory,
                        int requiredProcessors)
                 throws IOException

Description copied from interface: ClusterTaskScheduler

Submit a job.

Parameters:

jobName - job name

jobCommand - job command

jobDirectory - job directory

taskId - task id

requiredMemory - required memory

requiredProcessors - required processors

Returns:

a String with the id of the submitted job

Throws:

IOException - if an error occurs while submitting job

stopJob

public void stopJob(String jobId)
             throws IOException

Description copied from interface: ClusterTaskScheduler

Stop a job.

Parameters:

jobId - job id

Throws:

IOException - if an error occurs while stopping the job

statusJob

public ClusterTaskScheduler.StatusResult statusJob(String jobId)
                                            throws IOException

Description copied from interface: ClusterTaskScheduler

Get the status of a job.

Parameters:

jobId - job id

Throws:

IOException - if an error occurs while getting the status of the job

cleanupJob

public void cleanupJob(String jobId)
                throws IOException

Description copied from interface: ClusterTaskScheduler

Cleanup after a job.

Parameters:

jobId - job id

Throws:

IOException - if an error occurs while cleanup

additionalScriptEnvironment

protected Map<String,String> additionalScriptEnvironment()

Define additional environment variable for bpipe scripts.

Returns:

a Map with the additional environment variables