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

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main(String[]) - Static method in class biolockj.api.BioLockJ_API

main(String[]) - Static method in class biolockj.api.BuildDocs

For standard use case, pass in $BLJ/mkdocs/user-guide/docs/GENERATED

main(String[]) - Static method in class biolockj.BioLockJ

BioLockJ is the BioLockJ.jar Main-Class, and is the first method executed.
Execution summary:
Call BioLockJ.initBioLockJ(String[]) to assign pipeline root dir and log file If change password pipeline, call Email.encryptAndStoreEmailPassword() Otherwise execute BioLockJ.runPipeline()

main(String[]) - Static method in class biolockj.launch.DockerLaunchProcess

main(String[]) - Static method in class biolockj.launch.JavaLaunchProcess

main(String[]) - Static method in class biolockj.launch.Launcher

main(String[]) - Static method in class biolockj.launch.LaunchProcess

main(String[]) - Static method in class biolockj.launch.ProgressMsgDemo

main(String[]) - Static method in class biolockj.launch.Reset

Reset a pipeline.

main(String[]) - Static method in class biolockj.module.implicit.parser.r16s.RdpHierParser

For stand-alone testing outside of a BioLockJ pipeline.
arg 0 - comma-separated list of taxonomic levels
arg 1 - comma-separated list of input files (one or more)
arg 2 - path/to/dir where the outputs will be saved

main(String[]) - Static method in class biolockj.util.DockerUtil

Even outside of a BioLockJ instance, access the containerize() and decontainerze() methods.

main(String[]) - Static method in class biolockj.util.UpdateJavaDocs

Main method updates the JavaDocs to replace undesirable auto-generated text.

MAIN_DOCKER_IMAGE - Static variable in class biolockj.Constants

Docker image used for the BioLockJ head node.

MAIN_DOCKER_OWNER - Static variable in class biolockj.Constants

Docker hub account that owns the .

MAIN_SCRIPT_PREFIX - Static variable in interface biolockj.module.BioModule

Script prefix appended to start of file name to indicate the main script in the script directory.
Non-AWS pipelines execute worker scripts via executing the main shell script - named with the prefix: "MAIN_"

makeMapper() - Static method in class biolockj.util.DockerUtil

As version v1.3.18, the logic to do this mapping is not part of the DockerUtil class.

makeMessage() - Method in class biolockj.module.hello_world.Hello_Friends

Create a message based on the modules properties.

makeMessage() - Method in class biolockj.module.hello_world.Step5

Create a message based on the modules properties.

makeRunAllScript(List<BioModule>) - Static method in class biolockj.util.DownloadUtil

This script allows a user to run all R scripts together from a single script.

makeVolMap() - Method in class biolockj.util.paths.BasicDockerMapper

This map is a link between file paths inside the container (the containerized path) and paths outside the container (the decontainerized path).

MAPPING_FILE - Static variable in class biolockj.util.DemuxUtil

Config String property "demultiplexer.mapping" lists the path to the mapping file to match sequence headers to barcodes.

markComplete(BioModule) - Static method in class biolockj.util.ModuleUtil

Method creates a file named "biolockjComplete" in module root directory to document module has completed successfully.

markDownReturn - Static variable in class biolockj.Constants

When writing mark down files, use this as a new line to start a new paragraph.

markStarted(BioModule) - Static method in class biolockj.util.ModuleUtil

Method creates a file named "biolockjStarted" in module root directory to document module has completed successfully.

markStatus(String) - Method in class biolockj.module.JavaModuleImpl

This method sets the module status by saving the indicator file to the module root dir.

markStatus(String, String) - Static method in class biolockj.pipelines.PipelineUtil

Set the status of a module or pipeline using a status flag file.

markStatus(String) - Static method in class biolockj.pipelines.PipelineUtil

Set the status of a module or pipeline using a status flag file.

markStatus(BioModule, String) - Static method in class biolockj.pipelines.PipelineUtil

Set the status of a module using a status flag file.

MASTER_PREFIX - Static variable in class biolockj.Constants

Prefix added to the master Config file: "MASTER_"

MasterConfigUtil - Class in biolockj.util

Simple utility containing String manipulation and formatting functions.

MasterConfigUtil() - Constructor for class biolockj.util.MasterConfigUtil

MATCHED_EXPECTATION - Static variable in class biolockj.util.ValidationUtil

The last column in a the output file, "MATCHED_EXPECTATION", indicates if the referenced file met all expectations (PASS), or not (FAIL), or was not compared to any expectations (REPORT).

MD5 - Static variable in class biolockj.util.ValidationUtil

MemoryUtil - Class in biolockj.util

This Java memory report utility can be used to help identify memory leaks in the application.

MemoryUtil() - Constructor for class biolockj.util.MemoryUtil

MergeQiimeOtuTables - Class in biolockj.module.implicit.qiime

This BioModule will run immediately after QiimeClosedRefClassifier if multiple otu_table.biom files were created.

MergeQiimeOtuTables() - Constructor for class biolockj.module.implicit.qiime.MergeQiimeOtuTables

META_BARCODE_COLUMN - Static variable in class biolockj.util.MetaUtil

Config property "metadata.barcodeColumn"

META_COLUMN_DELIM - Static variable in class biolockj.util.MetaUtil

Config property: "metadata.columnDelim"

META_COMMENT_CHAR - Static variable in class biolockj.util.MetaUtil

Config property: "metadata.commentChar"

META_FILE_PATH - Static variable in class biolockj.util.MetaUtil

Config String property: "metadata.filePath"

META_FILENAME_COLUMN - Static variable in class biolockj.util.MetaUtil

Config property "metadata.fileNameColumn"

META_MERGED - Static variable in class biolockj.module.report.taxa.AddMetadataToTaxaTables

File suffix added to OTU table file name once merged with metadata.

META_NULL_VALUE - Static variable in class biolockj.util.MetaUtil

Config property: "metadata.nullValue"

META_REQUIRED - Static variable in class biolockj.util.MetaUtil

Config Boolean property: "metadata.required"

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

Config Positive integer property defines total metabat memory per sample.

METADATA_COL_DELIM - Static variable in class biolockj.util.MetaUtil

Default column delimiter = tab character

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

MetadataException - Exception in biolockj.exception

MetadataException is thrown if errors occur processing Metadata files.

MetadataException(String) - Constructor for exception biolockj.exception.MetadataException

Create standard error to throw for Metadata related errors.

MetadataWithoutFileException - Exception in biolockj.exception

MetadataWithoutFileException(String) - Constructor for exception biolockj.exception.MetadataWithoutFileException

METAPHLAN2_DB - Static variable in class biolockj.module.classifier.wgs.Metaphlan2Classifier

Config Directory property containing alternate database: "metaphlan2.db"
Must always be paired with "metaphlan2.mpa_pkl"

METAPHLAN2_MPA_PKL - Static variable in class biolockj.module.classifier.wgs.Metaphlan2Classifier

Config File property containing path to the mpa_pkl file used to reference an alternate DB "metaphlan2.mpa_pkl"
Must always be paired with "metaphlan2.db"

Metaphlan2Classifier - Class in biolockj.module.classifier.wgs

This BioModule builds the bash scripts used to execute metaphlan2.py to classify WGS sequences with MetaPhlAn2.

Metaphlan2Classifier() - Constructor for class biolockj.module.classifier.wgs.Metaphlan2Classifier

Metaphlan2Parser - Class in biolockj.module.implicit.parser.wgs

This BioModules parses Metaphlan2Classifier output reports to build standard OTU abundance tables.

Metaphlan2Parser() - Constructor for class biolockj.module.implicit.parser.wgs.Metaphlan2Parser

MetaphlanNode - Class in biolockj.node.wgs

This class represents one line of Metaphlan2Classifier output.

MetaphlanNode(String, String) - Constructor for class biolockj.node.wgs.MetaphlanNode

Build the OtuNode by extracting the OTU names for each level from the line.

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

Config Positive integer property defines total metaspades memory per sample.

MetaUtil - Class in biolockj.util

This utility is used to read, modify, or create a metadata file for the sequence data.

millisToMinutes(long) - Static method in class biolockj.util.BioLockJUtil

Convert milliseconds to minutes - useful to convert Java millisecond output rounded to the nearest minute.

minutesToMillis(int) - Static method in class biolockj.util.BioLockJUtil

Convert minutes to milliseconds - useful to convert Config props measure in minutes to milliseconds since many Java functions have milliseconds args.

MODULE_SEQ_PACKAGE - Static variable in class biolockj.Constants

BioLockJ SEQ module package: "biolockj.module.seq"

MODULE_WGS_CLASSIFIER_PACKAGE - Static variable in class biolockj.Constants

BioLockJ WGS Classifier module package: "biolockj.module.classifier.wgs"

moduleComplete() - Method in interface biolockj.module.JavaModule

This method will create the success flag file so the next module can run.

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

moduleExists(String) - Static method in class biolockj.util.ModuleUtil

Check if a module was in the pipeline at least once.

moduleFailed() - Method in interface biolockj.module.JavaModule

This method will create the fail flag file so the pipeline can move on..

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

moduleInfo() - Static method in class biolockj.api.BioLockJ_API

Returns a json formatted list of all modules and for each module that implements the gui interface, it lists the props used by the module, and for each prop the info.

ModuleUtil - Class in biolockj.util

This utility holds general methods useful for BioModule interaction and management.

mostRecent - Variable in class biolockj.launch.LaunchProcess

msgs - Variable in class biolockj.launch.LaunchProcess

multiplex(File) - Method in class biolockj.module.seq.Multiplexer

Add file sequences to the multiplexed file.

Multiplexer - Class in biolockj.module.seq

This BioModule will merge sequence files into a single combined sequence file, with either the sample ID or an identifying bar-code (if defined in the metatata) is stored in the sequence header.
BioLockJ is designed to run on demultiplexed data so this must be the last module to run in its branch.

Multiplexer() - Constructor for class biolockj.module.seq.Multiplexer

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