public class Constants extends Object
Modifier and Type | Field and Description |
---|---|
static long |
APP_START_TIME
Captures the application start time
|
static String |
ASSIGN_ALIAS
The key string to define an alias for an individual module: {@value
|
static String |
AWS_S3_XFER_TIMEOUT
Config Integer property: "aws.s3TransferTimeout" |
static String |
BASH_PROFILE
Bash profile fo;e name: ".bash_profile"
|
static String |
BASH_RC
Bashrc file name: ".bashrc"
|
static String |
BLJ_COMPLETE
Name of the file created in the BioModule or "internal.pipelineDir" root directory to indicate execution
was successful: "biolockjComplete"
|
static String |
BLJ_FAILED
Name of the file created in the "internal.pipelineDir" root directory to indicate fatal application
errors halted execution: "biolockjFailed"
|
static String |
BLJ_MODULE_TAG
Set "#BioModule" tag in
Config file to include in pipeline: "#BioModule"Example: #BioModule biolockj.module.ImportMetadata |
static String |
BLJ_STARTED
Name of the file created in the BioModule root directory to indicate execution has started: "biolockjStarted"
|
static String |
BLJ_VERSION_PROP
Config property: "biolockj.version""Property giving the biolockj version that was used to generate the config file." |
static String |
BLJ_VERSION_PROP_DESC |
static String |
BLJ_WIKI
URL to the BioLockJ WIKI
|
static String |
CLASS
Config option for "report.taxonomyLevels": "class" |
static String |
CLUSTER_HOST
|
static String |
DEFAULT_MOD_DEMUX
Config property: "pipeline.defaultDemultiplexer"
|
static String |
DEFAULT_MOD_FASTA_CONV
Config property: "pipeline.defaultFastaConverter"
|
static String |
DEFAULT_MOD_SEQ_MERGER
Config property: "pipeline.defaultSeqMerger"
|
static String |
DEFAULT_STATS_MODULE
Config property: "pipeline.defaultStatsModule"
|
static String |
DELIM_SEP
In an otu string for multiple levels, each separated by "|", each otu has a level prefix
ending with "__"
|
static String |
DETACH_JAVA_MODULES
Config property: "pipeline.detachJavaModules" |
static String |
DEVELOPER_NOTE
A prefix used for some messages.
|
static String |
DISABLE_ADD_IMPLICIT_MODULES
|
static String |
DISABLE_PRE_REQ_MODULES
Config property: "pipeline.disableAddPreReqModules" |
static String |
DOCKER_CONFIG_PATH
Config property: "${BLJ}/resources/config/default/docker.properties"
Default path for an additional configuration file used for any pipeline run in docker. |
static String |
DOCKER_EXE_PREFIX
Prefix used in several
Config String properties. |
static String |
DOMAIN
Config option for "report.taxonomyLevels": "domain" |
static String |
DOWNLOAD_DIR
Config String property: "pipeline.downloadDir" |
static String |
EXE_AWK
|
static String |
EXE_DOCKER
|
static String |
EXE_GZIP
|
static String |
EXE_JAVA
Config "executable" property: "exe.java" |
static String |
EXE_PREFIX
Prefix used in several
Config String properties. |
static String |
EXE_PYTHON
Config "executable" property: "exe.python" |
static String |
EXE_RSCRIPT
Config "executable" property: "exe.Rscript" |
static String |
FALSE
Boolean
Config property value option: "N" |
static String |
FAMILY
Config option for "report.taxonomyLevels": "family" |
static String |
FASTA
File extension for fasta files = "fasta"
|
static String |
FASTQ
File extension for fastq files: "fastq"
|
static String |
GENUS
Config option for "report.taxonomyLevels": "genus" |
static String |
GZIP_EXT
Gzip compressed file extension: ".gz"
|
static String |
HELP
Argument to print help menu: "-help"
|
static String |
HN2_DISABLE_GENE_FAMILIES
Config Boolean property: "humann2.disableGeneFamilies" |
static String |
HN2_DISABLE_PATH_ABUNDANCE
Config Boolean property: "humann2.disablePathAbundance" |
static String |
HN2_DISABLE_PATH_COVERAGE
Config Boolean property: "humann2.disablePathCoverage"
|
static String |
HN2_GENE_FAM_SUM
HumanN2 file suffix identifier for Gene Family Summary report: "geneFam"
|
static String |
HN2_PATH_ABUND_SUM
HumanN2 file suffix identifier for Pathway Abundance Summary report: "pAbund"
|
static String |
HN2_PATH_COVG_SUM
HumanN2 file suffix identifier for Pathway Coverage Summary report: "pCovg"
|
static String |
HN2_TOTAL_PATH_COUNT
HumanN2 meta column to store the total pathway count/sample: "Total_Pathways"
|
static String |
HN2_UNIQUE_PATH_COUNT
HumanN2 meta column to store the unique pathway count/sample: "Total_Pathways"
|
static String |
HOST_EXE_PREFIX
Prefix used in several
Config String properties. |
static String |
INDENT
Standard indent = 4 spaces.
|
static String |
INPUT_ALLOW_DUPS
Config boolean property: |
static String |
INPUT_DIRS
Config List property: "input.dirPaths" |
static String |
INPUT_FORWARD_READ_SUFFIX
Config String property: "input.suffixFw"Set file suffix used to identify forward reads in "input.dirPaths" |
static String |
INPUT_IGNORE_FILES
Config List property: "input.ignoreFiles" |
static String |
INPUT_REQUIRE_COMPLETE_PAIRS
Config Boolean property: "input.requireCompletePairs""Require all sequence input files have matching paired reads" |
(package private) static String |
INPUT_REQUIRE_COMPLETE_PAIRS_DESC |
static String |
INPUT_REVERSE_READ_SUFFIX
Config String property: "input.suffixRv"Set file suffix used to identify reverse reads in "input.dirPaths" |
static String |
INPUT_TRIM_PREFIX
Config String property: "input.trimPrefix" |
static String |
INPUT_TRIM_SUFFIX
Config String property: "input.trimSuffix" |
static String |
INPUT_TYPES
Config List property: "pipeline.inputTypes" |
static String |
INTERNAL_ALL_MODULES
Internal
Config List property: "internal.allModules"List of all configured, implicit, and pre/post-requisite modules for the pipeline. Example: biolockj.module.ImportMetadata, etc. |
static String |
INTERNAL_BLJ_MODULE
|
static String |
INTERNAL_DEFAULT_CONFIG
|
static String |
INTERNAL_IS_MULTI_LINE_SEQ
|
static String |
INTERNAL_MULTIPLEXED
Config Boolean property: "internal.multiplexed"Set to true if multiplexed reads are found, set by the application runtime code. |
static String |
INTERNAL_PAIRED_READS
Config Boolean property: "internal.pairedReads"Set to true if paired reads are found, set by the application runtime code. |
static String |
INTERNAL_PIPELINE_DIR
Config String property: "internal.pipelineDir"Stores the path of the pipeline root directory path set by the application runtime code. |
static String |
INTERNAL_PIPELINE_ID
Config String property: "internal.pipelineInstanceId"The pipeline instance id is generally formed from the pipeline name, the date the pipeline started and sometimes an additional integer to ensure an unique folder name. |
static String |
INTERNAL_PIPELINE_NAME
Config String property: "internal.pipelineName"Stores the name of the pipeline. |
static String |
INTERNAL_PREFIX
Any
Config property that starts with the "internal."
prefix will not be included in the final MASTER properties file. |
static String |
INTERNAL_SEQ_HEADER_CHAR
Config property: "internal.seqHeaderChar"The property holds the 1st character used in the sequence header for the given dataset |
static String |
INTERNAL_SEQ_TYPE
|
static String |
JAR_ARG
Java runtime arg used to pass application jar path: "-jar"
|
static String |
LIMIT_DEBUG_CLASSES
Config property used to limit classes that log debug statements when
"pipeline.logLevel"="Y"
TODO: make this clearer. |
static String |
LOG_EXT
BioLockJ log file extension: ".log"
|
static String |
LOG_LEVEL_PROPERTY
Config property used to set log sensitivity in
log4j.propertieslog4j.rootLogger=${pipeline.logLevel}, file, stdout DEBUG - Log all messages INFO - Log info, warning and error messages WARN - Log warning and error messages ERROR - Log error messages only |
static String |
LOG_SPACER
Spacer used to improve log file readability
|
static String |
MAIN_DOCKER_IMAGE
Docker image used for the BioLockJ head node.
|
static String |
MAIN_DOCKER_OWNER
Docker hub account that owns the .
|
static String |
markDownReturn
When writing mark down files, use this as a new line to start a new paragraph.
|
static String |
MASTER_PREFIX
Prefix added to the master Config file: "MASTER_"
|
static String |
MODULE_SEQ_PACKAGE
BioLockJ SEQ module package: "biolockj.module.seq"
|
static String |
MODULE_WGS_CLASSIFIER_PACKAGE
BioLockJ WGS Classifier module package: "biolockj.module.classifier.wgs"
|
static String |
ORDER
Config option for "report.taxonomyLevels": "order" |
static String |
OTU_COUNT
Included in the file name of each file output.
|
static String |
OTU_SEPARATOR
A pipe is used to separate each taxa "|"
|
static String |
OTU_TABLE_PREFIX
QIIME OTU table prefix: "otu_table"
|
static String |
P_VAL_CUTOFF
Config property "r.pvalCutoff" defines the p-value cutoff for significance |
static String |
PDF_EXT
BioLockJ PDF file extension: ".pdf"
|
static String |
PHYLUM
Config option for "report.taxonomyLevels": "phylum" |
static String |
PIPELINE_COPY_FILES
Config property: "pipeline.copyInput" |
static String |
PIPELINE_DEFAULT_PROPS
Config String property: "pipeline.defaultProps" |
static String |
PIPELINE_DESC
Config property to allow a free-hand description to a pipeline: "pipeline.desc" TODO:
needs to be implemented. |
static String |
PIPELINE_ENV
Config String property: "pipeline.env" |
static String |
PIPELINE_ENV_AWS
|
static String |
PIPELINE_ENV_CLUSTER
|
static String |
PIPELINE_ENV_LOCAL
Config option for property: "pipeline.env"Used to indicate running on a local machine (laptop, etc): "local" |
static String |
PIPELINE_ENV_VARS
Config List property: "pipeline.env" |
static String |
PIPELINE_ENV_VARS_DESC |
static String |
PIPELINE_LOCATION_KEY
Indicator for related programs (bash code, sheepdog_testing_suite) of the pipelines path: "Pipeline root directory: "
|
static String |
PIPELINE_NAME
Config property to assign a name to a pipeline: "pipeline.name" TODO: needs to be
implemented. |
protected static String |
PIPELINE_PRIVS
Config property: "pipeline.permissions"
|
static String |
PIPELINE_USE_EVARS
|
static String |
PIPELINE_USE_EVARS_DESC |
static String |
PRECHECK_COMPLETE
Name of the file created in the BioModule root directory to indicate the precheck
process encountered an error (if running in precheck mode): "precheckComplete"
|
static String |
PRECHECK_FAILED
Name of the file created in the BioModule root directory to indicate the precheck
process has completed (if running in precheck mode): "precheckFailed"
|
static String |
PRECHECK_STARTED
Name of the file created in the BioModule root directory to indicate the precheck
process has started (if running in precheck mode): "precheckStarted"
|
static String |
PROCESSED
File suffix appended to processed samples in the module output directory: "_reported.tsv"
|
static String |
PROJECT_DEFAULT_PROPS
Config String property: "project.defaultProps"Set file path of default property file. |
static String |
PROJECT_DESC
Config property to assign a free-hand to a project: "project.description" TODO: needs to be
implemented. |
static String |
PROJECT_NAME
Config property to assign a name to a project: "project.name" TODO: needs to be
implemented. |
static String |
PROPS_EXT
BioLockJ properties file extension: ".properties"
|
static String |
QIIME
QIIME application: "qiime"
|
static String |
QIIME_ALPHA_DIVERSITY_METRICS
Config list property to calculate alpha diversity metrics.For complete list of skbio.diversity.alpha options, see http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html "qiime.alphaMetrics" |
static String[] |
QIIME_AMBIGUOUS_TAXA
Qiime may find ambiguous taxa identified in various formats in different databases.
|
static String |
QIIME_BARCODE_SEQ_COL
QIIME mapping file required 2nd column name
|
static String |
QIIME_DEMUX_COL
QIIME mapping column created by
BuildQiimeMapping that stores the name of
the original fasta file associated with the sample: "BioLockJFileName" |
static String |
QIIME_DESC_COL
QIIME mapping file required name of last column
|
static String |
QIIME_LINKER_PRIMER_SEQ_COL
QIIME mapping file required 3rd column name
|
static String |
R_COLOR_BASE
Config property "r.colorBase" |
static String |
R_COLOR_FILE
Config property "r.colorFile" gives the path to a tab-delimited file giving the color
to use for each value of each metadata filed plotted. |
static String |
R_COLOR_HIGHLIGHT
Config property "r.colorHighlight" defines the highlight label color |
static String |
R_COLOR_PALETTE
Config property "r.colorPalette" defines the color palette for PDF plots |
static String |
R_COLOR_POINT
Config property "r.colorPoint" defines the pch point colors for PDF plots |
static String |
R_DEBUG
Config boolean property "r.debug" sets the debug log function enabled |
static String |
R_EXT
File extension of BioLockJ generated R Scripts: ".R"
|
static String |
R_FUNCTION_LIB
This library script contains helper functions used in the R scripts: "BioLockJ_Lib.R"
|
static String |
R_INTERNAL_RUN_HN2
Config Boolean property to signal R scripts to build HumanN2 reports |
static String |
R_MAIN_SCRIPT
This main R script that sources helper libraries and calls modules main method function: "BioLockJ_MAIN.R"
|
static String |
R_PCH
Config property "r.pch" defines the plot point shape for PDF plots |
static String |
R_RARE_OTU_THRESHOLD
Config Double property "r.rareOtuThreshold" defines number OTUs needed to includ in
reports |
static String |
R_SAVE_R_DATA
Config boolean property "r.saveRData" enables the .RData file to save. |
static String |
R_TIMEOUT
Config property "r.timeout": |
static String |
R_USE_UINQUE_COLORS |
static String |
RDP_THRESHOLD_SCORE
Config String property: "rdp.minThresholdScore"RdpParser will ignore OTU assignments below the threshold score (0-100) |
static String |
REPORT_LOG_BASE
Config String property: "report.logBase"Required to be set to "e" or "10" to build log normalized reports. |
static String |
REPORT_MIN_COUNT
Config Positive Integer property "report.minCount" defines the minimum table count
allowed, if a count less that this value is found, it is set to 0. |
static String |
REPORT_NUM_HITS
Config Boolean property: "report.numHits"If set to "Y", NUM_OTUS will be added to metadata file by ParserModuleImpl and included in R reports |
static String |
REPORT_NUM_READS
|
static String |
REPORT_SAMPLE_CUTOFF
Config Positive Double property "report.scarceSampleCutoff" defines minimum percentage of
data columns must be non-zero to keep the sample. |
static String |
REPORT_SCARCE_CUTOFF
Config Positive Double property "report.scarceCountCutoff" defines minimum percentage of
samples that must contain a count value for it to be kept. |
static String |
REPORT_TAXONOMY_LEVELS
Config List property: "report.taxonomyLevels"This property drives a lot of BioLockJ functionality and determines which taxonomy-levels are reported. |
static String |
REPORT_UNCLASSIFIED_TAXA
Config Boolean property: "report.unclassifiedTaxa" |
static String |
RETURN
Return character: *backslash-n*
|
static String |
RM_TEMP_FILES
Config property: "pipeline.deleteTempFiles" |
static String |
RSCRIPT
Rscript exe commmand.
|
static String |
SCRIPT_DEFAULT_HEADER
Config List property: "script.defaultHeader""Store default script header for MAIN script and locally run WORKER scripts." |
static String |
SCRIPT_DEFAULT_HEADER_DESC |
static String |
SCRIPT_DELAY_FOR_FILE_UPDATES
Config List property: "script.fileRefreshDelay"In some cases, especially with virtualization, there may be delays between before the program is able to register file system changes made by another container/node/host. |
static String |
SCRIPT_DIR
Name of the script sub-directory: "script"
|
static String |
SCRIPT_FAILURES
File suffix appended to failed scripts: "Failures"
|
static String |
SCRIPT_NUM_THREADS
Config Integer property: "script.numThreads""Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter." |
static String |
SCRIPT_NUM_THREADS_DESC |
static String |
SCRIPT_NUM_WORKERS
Config Integer property: "script.numWorkers""Set number of samples to process per script (if parallel processing)" |
static String |
SCRIPT_NUM_WORKERS_DESC |
static String |
SCRIPT_PERMISSIONS
|
static String |
SCRIPT_PERMISSIONS_DESC |
static String |
SCRIPT_STARTED
File suffix appended to started script: "Started"
|
static String |
SCRIPT_SUCCESS
File suffix appended to successful scripts: "Success"
|
static String |
SCRIPT_TIMEOUT
|
static String |
SCRIPT_TIMEOUT_DESC |
static String |
SET_SEED
Config property "pipeline.setSeed" |
static String |
SH_EXT
BioLockJ shell script file extension: ".sh"
|
static String |
SPECIES
Config option for "report.taxonomyLevels": "species" |
static String |
STANDARD_CONFIG_PATH
Default
Config imported for all pipelines (if file exists) |
static String |
STATUS_MARK_KEY
Key used in standard err messages indicating that this line should be shown to the user.
|
static String |
STATUS_START_KEY
Key used in standard err messages indicating that this line should be shown to the user.
|
static String |
TAB_DELIM
BioLockJ tab character: "\t"
|
static String |
TRUE
Boolean
Config property value option: "Y" |
static String |
TSV_EXT
BioLockJ tab delimited text file extension: ".tsv"
|
static String |
TXT_EXT
BioLockJ standard text file extension: ".txt"
|
static String |
UNCLASSIFIED
Unclassified taxa prefix: "Unclassified"
|
static String |
UNVERIFIED_PROPS_FILE |
static String |
USER_PROFILE
Config File property: "pipeline.userProfile" |
static String |
VALIDATION_ENABLED
String used by sheepdog_testing_suite to assert that validation is enabled: "This pipeline has validation enabled.".
|
static String |
VERSION
BioLockJ main() runtime arg used to print version info: "-version"
|
static String |
YEAR_AND_OWNER
The year and owner of this program as of most recent development.
|
Constructor and Description |
---|
Constants() |
Modifier and Type | Method and Description |
---|---|
(package private) static void |
registerProps()
Register properties with the Properties class for API access.
|
public static final long APP_START_TIME
public static final String ASSIGN_ALIAS
public static final String AWS_S3_XFER_TIMEOUT
Config
Integer property: "aws.s3TransferTimeout"public static final String BASH_PROFILE
public static final String BASH_RC
public static final String BLJ_COMPLETE
public static final String BLJ_FAILED
public static final String BLJ_MODULE_TAG
Config
file to include in pipeline: "#BioModule"public static final String BLJ_STARTED
public static final String BLJ_VERSION_PROP
Config
property: "biolockj.version"public static final String BLJ_VERSION_PROP_DESC
public static final String BLJ_WIKI
public static final String CLASS
Config
option for "report.taxonomyLevels": "class"public static final String CLUSTER_HOST
public static final String DEFAULT_MOD_DEMUX
Config
property: "pipeline.defaultDemultiplexer"
public static final String DEFAULT_MOD_FASTA_CONV
Config
property: "pipeline.defaultFastaConverter"
public static final String DEFAULT_MOD_SEQ_MERGER
Config
property: "pipeline.defaultSeqMerger"
public static final String DEFAULT_STATS_MODULE
Config
property: "pipeline.defaultStatsModule"
public static final String DELIM_SEP
public static final String DETACH_JAVA_MODULES
Config
property: "pipeline.detachJavaModules"public static final String DEVELOPER_NOTE
public static final String DISABLE_ADD_IMPLICIT_MODULES
public static final String DISABLE_PRE_REQ_MODULES
Config
property: "pipeline.disableAddPreReqModules"public static final String DOCKER_CONFIG_PATH
Config
property: "${BLJ}/resources/config/default/docker.properties"
Default path for an additional configuration file used for any pipeline run in docker.public static final String DOCKER_EXE_PREFIX
Config
String properties. "dockerExe."EXE_PREFIX
,
Constant Field Valuespublic static final String DOMAIN
Config
option for "report.taxonomyLevels": "domain"public static final String DOWNLOAD_DIR
Config
String property: "pipeline.downloadDir"public static final String EXE_PREFIX
Config
String properties. "exe."public static final String EXE_AWK
public static final String EXE_DOCKER
public static final String EXE_GZIP
public static final String EXE_JAVA
Config
"executable" property: "exe.java"public static final String EXE_PYTHON
Config
"executable" property: "exe.python"public static final String EXE_RSCRIPT
Config
"executable" property: "exe.Rscript"public static final String FALSE
Config
property value option: "N"public static final String FAMILY
Config
option for "report.taxonomyLevels": "family"public static final String FASTA
public static final String FASTQ
public static final String GENUS
Config
option for "report.taxonomyLevels": "genus"public static final String GZIP_EXT
public static final String HELP
public static final String HOST_EXE_PREFIX
Config
String properties. "hostExe."EXE_PREFIX
,
Constant Field Valuespublic static final String HN2_DISABLE_GENE_FAMILIES
Config
Boolean property: "humann2.disableGeneFamilies"public static final String HN2_DISABLE_PATH_ABUNDANCE
Config
Boolean property: "humann2.disablePathAbundance"public static final String HN2_DISABLE_PATH_COVERAGE
Config
Boolean property: "humann2.disablePathCoverage"
public static final String HN2_GENE_FAM_SUM
public static final String HN2_PATH_ABUND_SUM
public static final String HN2_PATH_COVG_SUM
public static final String HN2_TOTAL_PATH_COUNT
public static final String HN2_UNIQUE_PATH_COUNT
public static final String INDENT
public static final String INPUT_ALLOW_DUPS
Config
boolean property: public static final String INPUT_DIRS
Config
List property: "input.dirPaths"public static final String INPUT_FORWARD_READ_SUFFIX
Config
String property: "input.suffixFw"public static final String INPUT_IGNORE_FILES
Config
List property: "input.ignoreFiles"public static final String INPUT_REQUIRE_COMPLETE_PAIRS
Config
Boolean property: "input.requireCompletePairs"static final String INPUT_REQUIRE_COMPLETE_PAIRS_DESC
public static final String INPUT_REVERSE_READ_SUFFIX
Config
String property: "input.suffixRv"public static final String INPUT_TRIM_PREFIX
Config
String property: "input.trimPrefix"public static final String INPUT_TRIM_SUFFIX
Config
String property: "input.trimSuffix"public static final String INPUT_TYPES
Config
List property: "pipeline.inputTypes"public static final String INTERNAL_PREFIX
Config
property that starts with the "internal."
prefix will not be included in the final MASTER properties file.public static final String INTERNAL_ALL_MODULES
Config
List property: "internal.allModules"public static final String INTERNAL_BLJ_MODULE
public static final String INTERNAL_DEFAULT_CONFIG
public static final String INTERNAL_IS_MULTI_LINE_SEQ
Config
Internal Boolean property: "internal.isMultiLineSeq"SeqUtil
determines input sequences are multi-line format.public static final String INTERNAL_MULTIPLEXED
Config
Boolean property: "internal.multiplexed"public static final String INTERNAL_PAIRED_READS
Config
Boolean property: "internal.pairedReads"public static final String INTERNAL_PIPELINE_DIR
Config
String property: "internal.pipelineDir"public static final String INTERNAL_PIPELINE_NAME
Config
String property: "internal.pipelineName"public static final String INTERNAL_PIPELINE_ID
Config
String property: "internal.pipelineInstanceId"public static final String INTERNAL_SEQ_HEADER_CHAR
Config
property: "internal.seqHeaderChar"public static final String INTERNAL_SEQ_TYPE
Config
Internal property: "internal.seqType"public static final String JAR_ARG
public static final String LIMIT_DEBUG_CLASSES
Config
property used to limit classes that log debug statements when
"pipeline.logLevel"="Y"
TODO: make this clearer. Are these the classes that will log debug, or the classes that will be 'limited' ?public static final String LOG_EXT
public static final String LOG_LEVEL_PROPERTY
Config
property used to set log sensitivity in
log4j.propertiespublic static final String LOG_SPACER
public static final String MAIN_DOCKER_IMAGE
public static final String MAIN_DOCKER_OWNER
public static final String markDownReturn
public static final String MASTER_PREFIX
public static final String MODULE_SEQ_PACKAGE
public static final String MODULE_WGS_CLASSIFIER_PACKAGE
public static final String ORDER
Config
option for "report.taxonomyLevels": "order"public static final String OTU_COUNT
public static final String OTU_SEPARATOR
public static final String OTU_TABLE_PREFIX
public static final String PDF_EXT
public static final String PHYLUM
Config
option for "report.taxonomyLevels": "phylum"public static final String PIPELINE_COPY_FILES
Config
property: "pipeline.copyInput"public static final String PIPELINE_DEFAULT_PROPS
Config
String property: "pipeline.defaultProps"public static final String PIPELINE_DESC
Config
property to allow a free-hand description to a pipeline: "pipeline.desc" TODO:
needs to be implemented.public static final String PIPELINE_ENV
Config
String property: "pipeline.env"public static final String PIPELINE_ENV_VARS
Config
List property: "pipeline.env"public static final String PIPELINE_ENV_VARS_DESC
public static final String PIPELINE_USE_EVARS
Config
List property: "pipeline.useEnvVars"public static final String PIPELINE_USE_EVARS_DESC
public static final String PIPELINE_ENV_AWS
public static final String PIPELINE_ENV_CLUSTER
public static final String PIPELINE_ENV_LOCAL
Config
option for property: "pipeline.env"public static final String PIPELINE_LOCATION_KEY
public static final String PIPELINE_NAME
Config
property to assign a name to a pipeline: "pipeline.name" TODO: needs to be
implemented.protected static final String PIPELINE_PRIVS
Config
property: "pipeline.permissions"
public static final String PRECHECK_COMPLETE
public static final String PRECHECK_FAILED
public static final String PRECHECK_STARTED
public static final String PROCESSED
public static final String PROJECT_DEFAULT_PROPS
Config
String property: "project.defaultProps"public static final String PROJECT_DESC
Config
property to assign a free-hand to a project: "project.description" TODO: needs to be
implemented.public static final String PROJECT_NAME
Config
property to assign a name to a project: "project.name" TODO: needs to be
implemented.public static final String PROPS_EXT
public static final String QIIME
public static final String QIIME_ALPHA_DIVERSITY_METRICS
Config
list property to calculate alpha diversity metrics.public static final String[] QIIME_AMBIGUOUS_TAXA
public static final String QIIME_BARCODE_SEQ_COL
public static final String QIIME_DEMUX_COL
BuildQiimeMapping
that stores the name of
the original fasta file associated with the sample: "BioLockJFileName"public static final String QIIME_DESC_COL
public static final String QIIME_LINKER_PRIMER_SEQ_COL
public static final String R_EXT
public static final String P_VAL_CUTOFF
Config
property "r.pvalCutoff" defines the p-value cutoff for significancepublic static final String R_COLOR_BASE
Config
property "r.colorBase"public static final String R_COLOR_FILE
Config
property "r.colorFile" gives the path to a tab-delimited file giving the color
to use for each value of each metadata filed plotted.public static final String R_COLOR_HIGHLIGHT
Config
property "r.colorHighlight" defines the highlight label colorpublic static final String R_COLOR_PALETTE
Config
property "r.colorPalette" defines the color palette for PDF plotspublic static final String R_COLOR_POINT
Config
property "r.colorPoint" defines the pch point colors for PDF plotspublic static final String R_DEBUG
Config
boolean property "r.debug" sets the debug log function enabledpublic static final String R_FUNCTION_LIB
public static final String R_MAIN_SCRIPT
public static final String R_PCH
Config
property "r.pch" defines the plot point shape for PDF plotspublic static final String R_RARE_OTU_THRESHOLD
Config
Double property "r.rareOtuThreshold" defines number OTUs needed to includ in
reportspublic static final String R_SAVE_R_DATA
Config
boolean property "r.saveRData" enables the .RData file to save.public static final String R_USE_UINQUE_COLORS
public static final String R_TIMEOUT
Config
property "r.timeout": public static final String R_INTERNAL_RUN_HN2
Config
Boolean property to signal R scripts to build HumanN2 reportspublic static final String RDP_THRESHOLD_SCORE
Config
String property: "rdp.minThresholdScore"public static final String REPORT_LOG_BASE
Config
String property: "report.logBase"public static final String REPORT_MIN_COUNT
Config
Positive Integer property "report.minCount" defines the minimum table count
allowed, if a count less that this value is found, it is set to 0.public static final String REPORT_NUM_HITS
Config
Boolean property: "report.numHits"ParserModuleImpl
and included in R reportspublic static final String REPORT_NUM_READS
Config
Boolean property: "report.numReads"public static final String REPORT_SAMPLE_CUTOFF
Config
Positive Double property "report.scarceSampleCutoff" defines minimum percentage of
data columns must be non-zero to keep the sample.public static final String REPORT_SCARCE_CUTOFF
Config
Positive Double property "report.scarceCountCutoff" defines minimum percentage of
samples that must contain a count value for it to be kept.public static final String REPORT_TAXONOMY_LEVELS
Config
List property: "report.taxonomyLevels"public static final String REPORT_UNCLASSIFIED_TAXA
Config
Boolean property: "report.unclassifiedTaxa"public static final String RETURN
public static final String RM_TEMP_FILES
Config
property: "pipeline.deleteTempFiles"public static final String RSCRIPT
public static final String SCRIPT_DEFAULT_HEADER
Config
List property: "script.defaultHeader"public static final String SCRIPT_DEFAULT_HEADER_DESC
public static final String SCRIPT_DELAY_FOR_FILE_UPDATES
Config
List property: "script.fileRefreshDelay"public static final String SCRIPT_DIR
public static final String SCRIPT_FAILURES
public static final String SCRIPT_NUM_THREADS
Config
Integer property: "script.numThreads"public static final String SCRIPT_NUM_THREADS_DESC
public static final String SCRIPT_NUM_WORKERS
Config
Integer property: "script.numWorkers"public static final String SCRIPT_NUM_WORKERS_DESC
public static final String SCRIPT_PERMISSIONS
public static final String SCRIPT_PERMISSIONS_DESC
public static final String SCRIPT_STARTED
public static final String SCRIPT_SUCCESS
public static final String SCRIPT_TIMEOUT
public static final String SCRIPT_TIMEOUT_DESC
public static final String SET_SEED
Config
property "pipeline.setSeed"public static final String SH_EXT
public static final String SPECIES
Config
option for "report.taxonomyLevels": "species"public static final String STANDARD_CONFIG_PATH
Config
imported for all pipelines (if file exists)public static final String STATUS_MARK_KEY
ProgressUtil
; lines with this key will be used print a line at launch replacing any current spinner.
This should be used to mark the completion of a potentially lengthy process was used STATUS_START_KEY
at the start.STATUS_START_KEY
,
Constant Field Valuespublic static final String STATUS_START_KEY
ProgressUtil
; lines with this key will be used to start a spinner,
and should be printed at the start of a potentially lengthy process.STATUS_MARK_KEY
,
Constant Field Valuespublic static final String TAB_DELIM
public static final String TRUE
Config
property value option: "Y"public static final String TSV_EXT
public static final String TXT_EXT
public static final String UNCLASSIFIED
public static final String USER_PROFILE
Config
File property: "pipeline.userProfile"public static final String VERSION
public static final String VALIDATION_ENABLED
public static final String UNVERIFIED_PROPS_FILE
public static final String YEAR_AND_OWNER
static final void registerProps() throws API_Exception
API_Exception