A B C D E F G H I J K L M N O P Q R S T U V W X Y

E

EC2_ACQUISITION_STRATEGY - Static variable in class biolockj.util.NextflowUtil

Config String property: "aws.ec2AcquisitionStrategy"

EC2_INSTANCE_TYPE - Static variable in class biolockj.util.NextflowUtil

Config String property: "aws.ec2InstanceType"

EdgeR - Class in biolockj.module.rnaseq

EdgeR() - Constructor for class biolockj.module.rnaseq.EdgeR

Email - Class in biolockj.module.report

This BioModule is used to email the user the pipeline execution status and summary.

Email() - Constructor for class biolockj.module.report.Email

EMAIL_ENCRYPTED_PASSWORD - Static variable in class biolockj.module.report.Email

Config String property: "mail.encryptedPassword"

EMAIL_FROM - Static variable in class biolockj.module.report.Email

Config String property: "mail.from"

EMAIL_HOST - Static variable in class biolockj.module.report.Email

Config String property: "mail.smtp.host"
Session SMTP host

EMAIL_PORT - Static variable in class biolockj.module.report.Email

Config Integer property: "mail.smtp.port"
Session SMTP port

EMAIL_SMTP_AUTH - Static variable in class biolockj.module.report.Email

Config Boolean property: "mail.smtp.auth"
Session SMTP authorization flag, set to "Y" if required by "mail.smtp.host"

EMAIL_START_TLS_ENABLE - Static variable in class biolockj.module.report.Email

Config Boolean property: "mail.smtp.starttls.enable"
Session SMTP TLS enable flag, set to "Y" if required by "mail.smtp.host"

EMAIL_TO - Static variable in class biolockj.module.report.Email

Config List property: "mail.to" This property defines the email recipients

enableLogs(boolean) - Static method in class biolockj.Log

Boolean toggle to enable/disable all log messages TODO: when is this a good idea?

encrypt(String) - Static method in class biolockj.module.report.Email

Encrypt clear-text password

encryptAndStoreEmailPassword() - Static method in class biolockj.module.report.Email

Read clear-text password by call to RuntimeParamUtil.getAdminEmailPassword()
Encrypt password by call to Email.encrypt(String)

EndLaunch - Exception in biolockj.launch

EndLaunch(int) - Constructor for exception biolockj.launch.EndLaunch

EndLaunch(int, String) - Constructor for exception biolockj.launch.EndLaunch

EndLaunch(String) - Constructor for exception biolockj.launch.EndLaunch

EndLaunch(int, List<String>) - Constructor for exception biolockj.launch.EndLaunch

EndLaunch(List<String>) - Constructor for exception biolockj.launch.EndLaunch

ENV_ARG - Static variable in class biolockj.launch.LaunchProcess

envVars - Variable in class biolockj.launch.LaunchProcess

equals(Object) - Method in class biolockj.module.BioModuleImpl

Compared based on ID

equals(Object) - Method in class biolockj.node.JsonNode

equals(Object) - Method in class biolockj.node.ParsedSample

ERROR - Static variable in class biolockj.Log

ERROR log message type:

error(Class<?>, String) - Static method in class biolockj.Log

Print log level ERROR message without exception stacktrace

error(Class<?>, String, Exception) - Static method in class biolockj.Log

Print log level ERROR message.

ERROR_MSG - Static variable in class biolockj.exception.FatalExceptionHandler

ERROR_TYPE - Static variable in class biolockj.exception.FatalExceptionHandler

EXCITE_PROP - Static variable in class biolockj.module.hello_world.Hello_Friends

"The number of ! to use with the phrase."

EXCITE_PROP - Static variable in class biolockj.module.hello_world.Step3

"The number of ! to use with the phrase."

EXCITE_PROP_DESC - Static variable in class biolockj.module.hello_world.Hello_Friends

EXCITE_PROP_DESC - Static variable in class biolockj.module.hello_world.Step3

EXE_AWK - Static variable in class biolockj.Constants

Config "executable" property: "exe.awk"

EXE_CHECKM - Static variable in class biolockj.module.assembly.GenomeAssembly

Config exe property for checkm executable: "exe.checkm"

EXE_CHECKM_PARAMS - Static variable in class biolockj.module.assembly.GenomeAssembly

Config List property used to obtain the checkm runtime parameters: "exe.checkmParams"

EXE_DOCKER - Static variable in class biolockj.Constants

Config "executable" property: "exe.docker"

EXE_FASTERQ - Static variable in class biolockj.module.getData.sra.SraDownload

EXE_GZIP - Static variable in class biolockj.Constants

Config "executable" property: "exe.gzip"

EXE_HUMANN2 - Static variable in class biolockj.module.classifier.wgs.Humann2Classifier

Config "executable" property for humnan2 executable: "exe.humann2"

EXE_HUMANN2_JOIN_PARAMS - Static variable in class biolockj.module.classifier.wgs.Humann2Classifier

Config "list" property: "humann2.humann2JoinTableParams"

EXE_HUMANN2_PARAMS - Static variable in class biolockj.module.classifier.wgs.Humann2Classifier

Config "list" property: "humann2.humann2Params"

EXE_HUMANN2_RENORM_PARAMS - Static variable in class biolockj.module.classifier.wgs.Humann2Classifier

Config "list" property: "humann2.humann2RenormTableParams"

EXE_JAVA - Static variable in class biolockj.Constants

Config "executable" property: "exe.java"

EXE_KNEADDATA - Static variable in class biolockj.module.seq.KneadData

KneadData executable: "exe.kneaddata"

EXE_KNEADDATA_PARAMS - Static variable in class biolockj.module.seq.KneadData

Config property containing parameters for "exe.kneaddata": "kneaddata.kneaddataParams"

EXE_KRAKEN - Static variable in class biolockj.module.classifier.wgs.KrakenClassifier

Config exe property for kraken executable: "exe.kraken"

EXE_KRAKEN2 - Static variable in class biolockj.module.classifier.wgs.Kraken2Classifier

Config exe property for kraken2 executable: "exe.kraken2"

EXE_METABAT2 - Static variable in class biolockj.module.assembly.GenomeAssembly

Config exe property for metabat2 executable: "exe.metabat2"

EXE_METABAT2_PARAMS - Static variable in class biolockj.module.assembly.GenomeAssembly

Config List property used to obtain the metabat runtime parameters: "exe.metabat2Params"

EXE_METAPHLAN - Static variable in class biolockj.module.classifier.wgs.Metaphlan2Classifier

Config exe property used to obtain the metaphlan2 executable

EXE_METAPHLAN_PARAMS - Static variable in class biolockj.module.classifier.wgs.Metaphlan2Classifier

Config List property used to obtain the metaphlan2 executable params

EXE_METASPADES2 - Static variable in class biolockj.module.assembly.GenomeAssembly

Config exe property for metaspades executable: "exe.metaspades2"

EXE_METASPADES_PARAMS - Static variable in class biolockj.module.assembly.GenomeAssembly

Config List property used to obtain the metaspade runtime parameters: "exe.metaspade2Params"

EXE_PATH - Static variable in class biolockj.Properties

EXE_PEAR - Static variable in class biolockj.module.seq.PearMergeReads

Config property "exe.pear" defines the command line PEAR executable

EXE_PEAR_PARAMS - Static variable in class biolockj.module.seq.PearMergeReads

Config property "pearMergeReads.pearParams" is used to set the PEAR executable runtime parameters

EXE_PREFIX - Static variable in class biolockj.Constants

Prefix used in several Config String properties.

EXE_PYTHON - Static variable in class biolockj.Constants

Config "executable" property: "exe.python"

EXE_RSCRIPT - Static variable in class biolockj.Constants

Config "executable" property: "exe.Rscript"

EXE_VSEARCH - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier

Config property for vsearch exectuable used for chimera detection: "exe.vsearch"

EXE_VSEARCH_PARAMS - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier

Config property for "exe.vsearch" parameters (such as alternate reference database path): "qiime.vsearchParams"

executeModule() - Static method in class biolockj.Pipeline

Execute a single pipeline module.

executeModules() - Static method in class biolockj.Pipeline

This method executes all new and incomplete modules
Before/after a module is executed, set persistent module status by creating status indicator files.

executeTask() - Method in interface biolockj.module.BioModule

This is the main method called when it is time for the BioModule to complete its task.

executeTask() - Method in class biolockj.module.BioModuleImpl

executeTask() - Method in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier

Build the nested list of bash script lines that will be used by BashScriptBuilder to build the worker scripts.

executeTask() - Method in class biolockj.module.classifier.wgs.Humann2Classifier

Calling super to build scripts, then wait until any database downloads are complete before allowing the Pipeline to move forward and use these DB.

executeTask() - Method in class biolockj.module.implicit.ImportMetadata

If Config."metadata.filePath" is undefined, build a new metadata file with only 1 column of sample IDs.

executeTask() - Method in class biolockj.module.implicit.parser.r16s.RdpHierParser

executeTask() - Method in class biolockj.module.implicit.qiime.MergeQiimeOtuTables

Call MergeQiimeOtuTables.buildScript(List) to create bash script lines needed to merge "otu_table.biom"s with "merge_otu_tables.py" unless only 1 input file found, in which case, just copy it to the output dir.

executeTask() - Method in class biolockj.module.JavaModuleImpl

JavaModules run pure Java code.
If in Direct mode, execute JavaModuleImpl.runModule() to run the module functionality; another BioLockJ instance is the manager that has launched this instance to run this module.
Otherwise, this instance is the manager,
If Config."pipeline.detachJavaModules"="Y" execute BioModule.executeTask() to build the bash scripts to launch a secondary instance in direct mode to run this module.
Otherwise (if "pipeline.detachJavaModules"="N"), execute JavaModuleImpl.runModule() to run the Java code to execute module functionality within the manager instance.

executeTask() - Method in class biolockj.module.report.Email

Set status member variable and send email pipeline summary to email addresses listed in: Config."mail.to"

executeTask() - Method in class biolockj.module.report.r.R_Module

Builds an R script by calling sub-methods to builds the BaseScript and creates the MAIN script shell that sources the BaseScript, calls runProgram(), reportStatus() and main() which can only be implemented in a subclass.

executeTask() - Method in class biolockj.module.rnaseq.DESeq2

executeTask() - Method in class biolockj.module.rnaseq.EdgeR

executeTask() - Method in class biolockj.module.ScriptModuleImpl

Build the nested list of bash script lines that will be used by BashScriptBuilder to build the worker scripts.

executeTask() - Method in class biolockj.module.Stop

exeModule() - Static method in class biolockj.Pipeline

Return the BioModule currently being executed

exists() - Static method in class biolockj.util.MetaUtil

Check if metadata file exists

exitCode - Variable in exception biolockj.launch.EndLaunch

EXPECTATION_FILE - Static variable in class biolockj.util.ValidationUtil

Config String property giving the file path that gives the expected values for file metrics.

ExpectationFileFormatException - Exception in biolockj.exception

TODO : Add info

ExpectationFileFormatException(String, File) - Constructor for exception biolockj.exception.ExpectationFileFormatException

TODO : Add info

EXT_MODS_ARG - Static variable in class biolockj.launch.LaunchProcess

EXTERNAL_MODULES_CONTAINER_DIR - Static variable in class biolockj.launch.DockerLaunchProcess

A B C D E F G H I J K L M N O P Q R S T U V W X Y