- DatabaseModule - Interface in biolockj.module
-
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.
- DB_DIR - Static variable in class biolockj.module.getData.sra.SequenceReadArchive
-
- DB_DIR_DESC - Static variable in class biolockj.module.getData.sra.SequenceReadArchive
-
- DB_NAME - Static variable in class biolockj.module.getData.sra.SequenceReadArchive
-
- DEBUG - Static variable in class biolockj.Log
-
DEBUG log message type:
- debug(Class<?>, String) - Static method in class biolockj.Log
-
Print log level DEBUG message.
Do not print
MetaUtil debug since these will always print since the Logger isn't
initialized yet and logMesseges will print them as INFO after Log file initializes.
- DEBUG_ARG - Static variable in class biolockj.launch.LaunchProcess
-
- DEBUG_FLAG - Static variable in class biolockj.util.RuntimeParamUtil
-
Flag argument; if present, BioLockJ will set the Conig property to DEBUG.
- deContainerizePath(String) - Static method in class biolockj.util.DockerUtil
-
If running in docker mode, convert this path to the form that can be used on the host machine.
- deContainerizePath(File) - Static method in class biolockj.util.DockerUtil
-
- decrypt(String) - Method in class biolockj.module.report.Email
-
Used to authenticate the service email account defined in EMAIL_FROM.
- DEFAULT_COMMENT_CHAR - Static variable in class biolockj.util.MetaUtil
-
Default comment character for any new metadata file created by a BioModule: ""
- DEFAULT_DOCKER_MAPPER - Static variable in class biolockj.util.DockerUtil
-
- DEFAULT_FORMAT - Static variable in class biolockj.Log
-
Standard BioLockJ log format includes date, time, severity type, and calling class before the msg.
- DEFAULT_IMAGE_NAME - Static variable in class biolockj.util.DockerUtil
-
A light-weight docker image to use.
- DEFAULT_IMAGE_OWNER - Static variable in class biolockj.util.DockerUtil
-
- DEFAULT_IMAGE_TAG - Static variable in class biolockj.util.DockerUtil
-
- DEFAULT_MOD_DEMUX - Static variable in class biolockj.Constants
-
Config property: "pipeline.defaultDemultiplexer"
- DEFAULT_MOD_FASTA_CONV - Static variable in class biolockj.Constants
-
Config property: "pipeline.defaultFastaConverter"
- DEFAULT_MOD_SEQ_MERGER - Static variable in class biolockj.Constants
-
Config property: "pipeline.defaultSeqMerger"
- DEFAULT_NULL_VALUE - Static variable in class biolockj.util.MetaUtil
-
Default field value to represent null-value: "NA"
- DEFAULT_STATS_MODULE - Static variable in class biolockj.Constants
-
Config property: "pipeline.defaultStatsModule"
- DELIM_SEP - Static variable in class biolockj.Constants
-
In an otu string for multiple levels, each separated by
"|", each otu has a level prefix
ending with "__"
- delimToLevelMap() - Static method in class biolockj.node.OtuNodeImpl
-
Map level delimeter to level names.
- demultiplex(Map<String, Set<String>>) - Method in class biolockj.module.implicit.Demultiplexer
-
Demultiplex the file into separate small temp files, with
2000000 lines each for
processing.
- Demultiplexer - Class in biolockj.module.implicit
-
This BioModule splits multiplexed data into a separate file or pair of files (for paired reads) for each sample.
- Demultiplexer() - Constructor for class biolockj.module.implicit.Demultiplexer
-
- DEMUX_STRATEGY - Static variable in class biolockj.util.DemuxUtil
-
Config property "demultiplexer.strategy" tells BioLockJ how to match sequences with Sample
IDs.
Options: barcode_in_header, barcode_in_mapping, barcode_in_seq, id_in_header, do_not_demux.
If using barcodes, metadata column
"metadata.barcodeColumn" is required.
- DemuxUtil - Class in biolockj.util
-
This utility contains standard methods used to handle multiplexed data.
- DemuxUtil() - Constructor for class biolockj.util.DemuxUtil
-
- demuxWithBarcode() - Static method in class biolockj.util.DemuxUtil
-
Return TRUE if barcode column is defined in the Config file and is populated in the metadata file
- deprecatedPropMessage(String) - Static method in class biolockj.Properties
-
Returns a message telling the user that the property is deprecated.
- deregisterThread(Thread) - Static method in class biolockj.Processor
-
De-register a thread, so it is not considered when shutting down the application.
- DESeq2 - Class in biolockj.module.rnaseq
-
- DESeq2() - Constructor for class biolockj.module.rnaseq.DESeq2
-
- DEST_DIR - Static variable in class biolockj.module.getData.sra.SraDownload
-
- DETACH_JAVA_MODULES - Static variable in class biolockj.Constants
-
Config property: "pipeline.detachJavaModules"
- DEVELOPER_NOTE - Static variable in class biolockj.Constants
-
A prefix used for some messages.
- DIRECT_FORMAT - Static variable in class biolockj.Log
-
Direct BioLockJ log prefix includes only the msg.
- DIRECT_MODE - Static variable in class biolockj.util.RuntimeParamUtil
-
Direct mode runtime parameter switch: "-direct"
- DirectModuleException - Exception in biolockj.exception
-
Some module are run as secondary instances of the BioLockJ program.
- DirectModuleException(String) - Constructor for exception biolockj.exception.DirectModuleException
-
- DirectModuleException() - Constructor for exception biolockj.exception.DirectModuleException
-
- DIRECTORY - Static variable in exception biolockj.exception.ConfigPathException
-
One of 2 BioLockJ file path types that can be passed to the constructor "directory".
- DISABLE_ADD_IMPLICIT_MODULES - Static variable in class biolockj.Constants
-
- DISABLE_PRE_REQ_MODULES - Static variable in class biolockj.Constants
-
Config property: "pipeline.disableAddPreReqModules"
- discardPrecheckPipeline(File) - Static method in class biolockj.pipelines.PipelineUtil
-
- displayArgVals() - Method in class biolockj.launch.LaunchProcess
-
- displayAsciiArt() - Static method in class biolockj.util.SummaryUtil
-
Print the application name *bigly* with some ASCII art :-)
- displayID(BioModule) - Static method in class biolockj.util.ModuleUtil
-
Return the module ID as a 2 digit display number (add leading zero if needed).
- displayName(BioModule) - Static method in class biolockj.util.ModuleUtil
-
Return the name of the module (or an alias if it has one).
- displaySignature(BioModule) - Static method in class biolockj.util.ModuleUtil
-
- DO_GZIP - Static variable in class biolockj.module.seq.Multiplexer
-
Config boolean property: "multiplexer.gzip":
- DO_UPDATE - Static variable in class biolockj.module.getData.sra.SraMetaDB
-
Config property: "sra.forceDbUpdate"
- doChangePassword() - Static method in class biolockj.util.RuntimeParamUtil
-
Return TRUE if runtime parameters indicate change password request
- DOCKER_ARG - Static variable in class biolockj.launch.LaunchProcess
-
- DOCKER_BLJ_MOUNT_DIR - Static variable in class biolockj.util.DockerUtil
-
Docker container root user EFS directory: /mnt/efs
- DOCKER_CONFIG_PATH - Static variable in class biolockj.Constants
-
Config property: "${BLJ}/resources/config/default/docker.properties"
Default path for an additional configuration file used for any pipeline run in docker.
- DOCKER_DB_DIR - Static variable in class biolockj.util.DockerUtil
-
Docker container root user DB directory: /mnt/efs/db
- DOCKER_DEFAULT_DB_DIR - Static variable in class biolockj.util.DockerUtil
-
Docker container root user DB directory: /mnt/efs/db
- DOCKER_EXE_PREFIX - Static variable in class biolockj.Constants
-
Prefix used in several
Config String properties.
- DOCKER_FLAG - Static variable in class biolockj.util.RuntimeParamUtil
-
Flag argument; if present, BioLockJ will use a docker volume map.
- DOCKER_HUB_USER - Static variable in class biolockj.util.DockerUtil
-
Config String property: "docker.imageOwner"
Docker Hub URL:
https://hub.docker.com
By default the "biolockj" user is used to pull the standard modules, but advanced users can deploy their own
versions of these modules and add new modules in their own Docker Hub account.
- DOCKER_IMG - Static variable in class biolockj.util.DockerUtil
-
Config String property: "docker.imageName"
- DOCKER_IMG_VERSION - Static variable in class biolockj.util.DockerUtil
-
Config String property: "docker.imageTag"
- DOCKER_MAPPER - Static variable in class biolockj.util.RuntimeParamUtil
-
Argument giving the name of the class to use for the DockerMountMapper: "-docker-mapper"
- DOCKER_MAPPER_ARG - Static variable in class biolockj.launch.LaunchProcess
-
- DOCKER_MOUNT_SOCK - Static variable in class biolockj.util.DockerUtil
-
Config Boolean property: "docker.mountSock"
- DOCKER_PIPELINE_DIR - Static variable in class biolockj.util.DockerUtil
-
- DOCKER_USER - Static variable in class biolockj.util.DockerUtil
-
Docker container default $USER: "root"
- DockerImageException - Exception in biolockj.exception
-
- DockerImageException(BioModule, String, String) - Constructor for exception biolockj.exception.DockerImageException
-
- DockerLaunchProcess - Class in biolockj.launch
-
- DockerLaunchProcess(String[]) - Constructor for class biolockj.launch.DockerLaunchProcess
-
- DockerMountMapper - Interface in biolockj.util.paths
-
Introduced with BioLockJ v1.3.18.
- DockerUtil - Class in biolockj.util
-
DockerUtil for Docker integration.
- DockerUtil() - Constructor for class biolockj.util.DockerUtil
-
- DockerVolCreationException - Exception in biolockj.exception
-
- DockerVolCreationException(String) - Constructor for exception biolockj.exception.DockerVolCreationException
-
- DockerVolCreationException() - Constructor for exception biolockj.exception.DockerVolCreationException
-
- DockerVolCreationException(Exception) - Constructor for exception biolockj.exception.DockerVolCreationException
-
- DockerVolumeException - Exception in biolockj.exception
-
- DockerVolumeException(String) - Constructor for exception biolockj.exception.DockerVolumeException
-
- doDebug() - Static method in class biolockj.Log
-
Return TRUE if = DEBUG.
- doDemux() - Static method in class biolockj.util.DemuxUtil
-
Return TRUE if Config is setup to demultiplex the sequence data.
- DOMAIN - Static variable in class biolockj.Constants
-
- DOMAIN_DELIM - Static variable in class biolockj.node.OtuNodeImpl
-
Standard classifier output level delimiter for DOMAIN
- doRestart() - Static method in class biolockj.util.RuntimeParamUtil
-
Return TRUE if runtime parameters indicate attempt to restart pipeline
- DOWNLOAD_DIR - Static variable in class biolockj.Constants
-
Config String property: "pipeline.downloadDir"
- DOWNLOAD_LIST - Static variable in class biolockj.util.DownloadUtil
-
Name of the file holding the list of pipeline files to include when running
DownloadUtil
- downloadDB(String[], String) - Static method in class biolockj.util.DockerUtil
-
Download a database for a Docker container
- DownloadUtil - Class in biolockj.util
-
This utility is used to validate the metadata to help ensure the format is valid R script input.