biolockj.module

Interface DatabaseModule

All Superinterfaces:

BioModule

All Known Implementing Classes:

ClassifierModuleImpl, Humann2Classifier, KneadData, Kraken2Classifier, KrakenClassifier, Metaphlan2Classifier, QiimeClassifier, QiimeClosedRefClassifier, QiimeDeNovoClassifier, QiimeOpenRefClassifier, RdpClassifier

public interface DatabaseModule
extends BioModule

Interface for BioModules that use a reference database that is used by the DockerUtil to find the correct database directory to map to the container /db volume.

Field Summary

Fields inherited from interface biolockj.module.BioModule

MAIN_SCRIPT_PREFIX, OUTPUT_DIR, TEMP_DIR

Method Summary

Modifier and Type	Method and Description
File	getDB() Return database directory, if multiple databases are configured, they must share a common parent directory and the common parent directory is returned by this method.

Methods inherited from interface biolockj.module.BioModule

checkDependencies, cleanUp, executeTask, getID, getInputFiles, getModuleDir, getOutputDir, getPostRequisiteModules, getPreRequisiteModules, getSummary, getTempDir, init, isValidInputModule

Method Detail

getDB

File getDB()
    throws Exception

Return database directory, if multiple databases are configured, they must share a common parent directory and the common parent directory is returned by this method.

Returns:

Database directory

Throws:

Exception - thrown if any runtime error occurs