public class R_PlotOtus extends R_Module implements ApiModule
GZIP_EXT, LOG_EXT, PDF_EXT, RETURN, SH_EXT, TAB_DELIM, TSV_EXT, TXT_EXT
LOG_DIR, MAIN_SCRIPT_PREFIX, NO_VERSION, OUTPUT_DIR, RES_DIR, TEMP_DIR
Constructor and Description |
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R_PlotOtus() |
Modifier and Type | Method and Description |
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void |
checkDependencies()
Validate module dependencies:
Require
Config . exists
Require Config . is positive integer
Require Config . is positive integer
Verify Config . is positive integer if set
Start the AWS DB sync to S3 if a novel DB has been configure and
"aws.copyDbToS3" is enabled
|
String |
getCitationString()
At a minimum, this should return the name and/or url for the wrapped tool.
|
String |
getDescription()
Briefly describe what this module does.
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protected String |
getModulePrefix()
Returns that prefix to use for property names.
|
protected String |
getModuleRScriptName() |
List<String> |
getPreRequisiteModules()
Returns
#getStatPreReqs() unless the pipeline input is already a stats table. |
buildScript, calcTimeout, cleanUp, executeTask, getCustomScriptProp, getDockerImageName, getDockerImageOwner, getDockerImageTag, getFunctionLib, getFunctionLib, getModuleRScript, getTimeout, grapRUsedProps, requiredRPackages
buildScriptForPairedReads, getJobParams, getMainScript, getRuntimeParams, getScriptDir, getScriptErrors, getSummary, getWorkerScriptFunctions, hasScripts, isValidProp
addGeneralProperty, addGeneralProperty, addGeneralProperty, addNewProperty, addNewProperty, cacheInputFiles, compareTo, equals, findModuleInputFiles, getAlias, getDescription, getDetails, getFileCache, getID, getInputFiles, getLogDir, getMenuPlacement, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getPropDescMap, getPropType, getPropTypeMap, getResourceDir, getTempDir, getTitle, hashCode, init, isValidInputModule, listProps, setAlias, toString
clone, finalize, getClass, notify, notifyAll, wait, wait, wait
getDescription, getDetails, getMenuPlacement, getPropType, getTitle, isValidProp, listProps
cleanUp, executeTask, getAlias, getDockerImageName, getDockerImageOwner, getDockerImageTag, getID, getInputFiles, getLogDir, getMetadata, getModuleDir, getOutputDir, getPostRequisiteModules, getPropDefault, getResourceDir, getSummary, getTempDir, init, isValidInputModule, setAlias, version
public void checkDependencies() throws Exception
ScriptModuleImpl
Config
. exists
Config
. is positive integer
Config
. is positive integer
Config
. is positive integer if set
checkDependencies
in interface BioModule
checkDependencies
in class R_Module
Exception
- thrown if missing or invalid dependencies are foundpublic List<String> getPreRequisiteModules() throws Exception
#getStatPreReqs()
unless the pipeline input is already a stats table.getPreRequisiteModules
in interface BioModule
getPreRequisiteModules
in class BioModuleImpl
Exception
- if invalid Class names are returned as prerequisitespublic String getDescription()
ApiModule
getDetails
.getDescription
in interface ApiModule
public String getCitationString()
ApiModule
getCitationString
in interface ApiModule
protected String getModuleRScriptName()
getModuleRScriptName
in class R_Module
protected String getModulePrefix()
R_Module
getModulePrefix
in class R_Module