net.maizegenetics.pangenome.pipeline

Class BuildSLURMBatchScriptPlugin

net.maizegenetics.pangenome.pipeline.BuildSLURMBatchScriptPlugin

public class BuildSLURMBatchScriptPlugin

Constructor Detail

BuildSLURMBatchScriptPlugin

public BuildSLURMBatchScriptPlugin(@Nullable
                                   java.awt.Frame parentFrame,
                                   boolean isInteractive)

BuildSLURMBatchScriptPlugin

public BuildSLURMBatchScriptPlugin()

Method Detail

processData

@Nullable
public net.maizegenetics.plugindef.DataSet processData(@Nullable
                                                                 net.maizegenetics.plugindef.DataSet input)

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

getToolTipText

@NotNull
public java.lang.String getToolTipText()

inputKeyFile

@NotNull
public java.lang.String inputKeyFile()

Name of the inputKeyFile file to process.

Returns:

Input Key File

inputKeyFile

@NotNull
public BuildSLURMBatchScriptPlugin inputKeyFile(@NotNull
                                                         java.lang.String value)

Set Input Key File. Name of the inputKeyFile file to process.

Parameters:

value - Input Key File

Returns:

this plugin

readDir

@NotNull
public java.lang.String readDir()

Name of the Fasta/Fastq dir to process.

Returns:

Fasta or Fastq dir to process

readDir

@NotNull
public BuildSLURMBatchScriptPlugin readDir(@NotNull
                                                    java.lang.String value)

Set Fasta or Fastq dir to process. Name of the Fasta/Fastq dir to process.

Parameters:

value - Fasta or Fastq dir to process

Returns:

this plugin

numNodes

public int numNodes()

Number Of Nodes to be requested

Returns:

Num Nodes

numNodes

@NotNull
public BuildSLURMBatchScriptPlugin numNodes(int value)

Set Num Nodes. Number Of Nodes to be requested

Parameters:

value - Num Nodes

Returns:

this plugin

numCores

public int numCores()

Number Of Cores to be requested

Returns:

Num Cores

numCores

@NotNull
public BuildSLURMBatchScriptPlugin numCores(int value)

Set Num Cores. Number Of Cores to be requested

Parameters:

value - Num Cores

Returns:

this plugin

numConsecutiveJobs

public int numConsecutiveJobs()

Number Of Consecutive jobs to run.

Returns:

Num Consec Jobs

numConsecutiveJobs

@NotNull
public BuildSLURMBatchScriptPlugin numConsecutiveJobs(int value)

Set Num Consec Jobs. Number Of Consecutive jobs to run.

Parameters:

value - Num Consec Jobs

Returns:

this plugin

outputSLURMScript

@NotNull
public java.lang.String outputSLURMScript()

Name of the Output SLURM Script

Returns:

Output SLURM Script

outputSLURMScript

@NotNull
public BuildSLURMBatchScriptPlugin outputSLURMScript(@NotNull
                                                              java.lang.String value)

Set Output SLURM Script. Name of the Output SLURM Script

Parameters:

value - Output SLURM Script

Returns:

this plugin

outputTargetNameFile

@NotNull
public java.lang.String outputTargetNameFile()

Name of the Output Target Name File

Returns:

Output Target Name File

outputTargetNameFile

@NotNull
public BuildSLURMBatchScriptPlugin outputTargetNameFile(@NotNull
                                                                 java.lang.String value)

Set Output Target Name File. Name of the Output Target Name File

Parameters:

value - Output Target Name File

Returns:

this plugin

emailAddress

@NotNull
public java.lang.String emailAddress()

Email Address to send notification when done

Returns:

Email Address

emailAddress

@NotNull
public BuildSLURMBatchScriptPlugin emailAddress(@NotNull
                                                         java.lang.String value)

Set Email Address. Email Address to send notification when done

Parameters:

value - Email Address

Returns:

this plugin

loadConda

public boolean loadConda()

Load dependencies from conda

Returns:

Load From Conda

loadConda

@NotNull
public BuildSLURMBatchScriptPlugin loadConda(boolean value)

Set Load From Conda. Load dependencies from conda

Parameters:

value - Load From Conda

Returns:

this plugin