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

E

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"
The Base 64 encrypted password is stored in the Config file using this property.

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

Config String property: "mail.from"
Admin email address used to send user pipeline notifications.

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

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 getAdminEmailPassword()
Encrypt password by call to Email.encrypt(String)

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.

EXE_AWK - Static variable in class biolockj.Constants

Config String property: "exe.awk"
Set command line executable awk.

EXE_DOCKER - Static variable in class biolockj.Constants

Config String property "exe.docker"
Set command line executable docker

EXE_GZIP - Static variable in class biolockj.Constants

Config String property "exe.gzip"
Set command line executable gzip

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

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

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

Config List property used to obtain the humann2_join_tables executable params

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

Config List property used to obtain the humann2 executable params

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

Config List property used to obtain the humann2_renorm_table executable params

EXE_JAVA - Static variable in class biolockj.Constants

Config property for java executable: "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": "exe.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_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_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 "exe.pearParams" is used to set the PEAR executable runtime parameters

EXE_PYTHON - Static variable in class biolockj.Constants

Config property to python executable

EXE_RSCRIPT - Static variable in class biolockj.module.report.r.R_Module

Config property "exe.Rscript" defines the command line executable to call 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): "exe.vsearchParams"

executeModule(BioModule) - 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.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.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 Docker mode and not in Direct mode, execute BioModule.executeTask() to build the bash script.
If not in Docker mode AND on the cluster AND Config."pipeline.detachJavaModules"="Y" execute BioModule.executeTask() to build the bash script
Otherwise, execute JavaModuleImpl.runModule() to run the Java code to execute module functionality.

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.ScriptModuleImpl

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

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

Determine if metadata file exists

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