- SAMPLE_ID_SUFFIX_TRIM_DEFAULT - Static variable in class biolockj.util.DemuxUtil
-
Multiplexed files created by BioLockJ may add sample ID to the sequence header if no barcode is provided.
If sample ID is added, it is immediately followed by the character: "_"
This value can be used then to set
Config.
"input.trimSuffix"
- sampleIdInHeader() - Static method in class biolockj.util.DemuxUtil
-
Return TRUE if Config is setup to demultiplex the sequence data based on Sample IDs in the sequence headers.
- sampleIdToQiimeIdMap - Static variable in class biolockj.module.implicit.parser.r16s.QiimeParser
-
Convenience map, to convert Sample ID to Qiime ID
- sanitizeMasterConfig() - Static method in class biolockj.util.MasterConfigUtil
-
Remove unused properties from the MASTER config file.
- SAVE_CONTAINER_ON_EXIT - Static variable in class biolockj.util.DockerUtil
-
Config Boolean property: "docker.saveContainerOnExit"
- saveEfsDataToS3() - Static method in class biolockj.util.NextflowUtil
-
Save EFS data to S3 based on pipeline Config.
- saveMasterConfig() - Static method in class biolockj.util.MasterConfigUtil
-
Save a single version of the Config file with all inherited properties for the default config (if any exist).
- saveMasterConfig(Map<String, String>) - Static method in class biolockj.util.MasterConfigUtil
-
Save a single version of the Config file with all inherited properties for the default config (if any exist).
- saveModuleProps(BioModule) - Static method in class biolockj.Config
-
- saveNextflowLog() - Static method in class biolockj.util.NextflowUtil
-
Save a copy of the Nextflow log file to the Pipeline root directory
- saveNextflowSuccessFlag() - Static method in class biolockj.util.NextflowUtil
-
Save success flag, so after pipeline bash start script can stop/terminate S3 instances if successful.
- saveSummary(String) - Static method in class biolockj.util.SummaryUtil
-
Save the summary generated to the pipeline root directory.
- scanFirstLine(BufferedReader, File) - Static method in class biolockj.util.SeqUtil
-
This method returns the 1st non-empty line and moves the BufferedReader pointer to this line.
- scanForKeys(String) - Method in class biolockj.launch.DockerLaunchProcess
-
- scanForKeys(String) - Method in class biolockj.launch.LaunchProcess
-
Scan string for specific keys which warrant specific actions.
- SCRIPT - Static variable in class biolockj.module.diy.GenMod
-
Config property: "genMod.scriptPath"
- SCRIPT_ADD_ALPHA_DIVERSITY - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
- SCRIPT_ADD_LABELS - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
QIIME script that produces
"combined_seqs.fna", the multiplexed fasta file: "add_qiime_labels.py"
- SCRIPT_CALC_ALPHA_DIVERSITY - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
QIIME script that creates alpha diversity metrics file in output/
"alphaDiversity.txt":
"alpha_diversity.py"
- SCRIPT_DEFAULT_HEADER - Static variable in class biolockj.Constants
-
- SCRIPT_DEFAULT_HEADER_DESC - Static variable in class biolockj.Constants
-
- SCRIPT_DELAY_FOR_FILE_UPDATES - Static variable in class biolockj.Constants
-
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.
- SCRIPT_DIR - Static variable in class biolockj.Constants
-
Name of the script sub-directory: "script"
- SCRIPT_FAILURES - Static variable in class biolockj.Constants
-
File suffix appended to failed scripts: "Failures"
- SCRIPT_FILTER_OTUS - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
QIIME script used to remove chimeras detected by
"exe.vsearch": "filter_otus_from_otu_table.py"
- SCRIPT_JOB_HEADER - Static variable in class biolockj.util.BashScriptBuilder
-
Config String property: "cluster.jobHeader"
- SCRIPT_MERGE_OTU_TABLES - Static variable in class biolockj.module.implicit.qiime.MergeQiimeOtuTables
-
QIIME script to merge multiple OTU tables in biom format.
- SCRIPT_NUM_THREADS - Static variable in class biolockj.Constants
-
- SCRIPT_NUM_THREADS_DESC - Static variable in class biolockj.Constants
-
- SCRIPT_NUM_WORKERS - Static variable in class biolockj.Constants
-
- SCRIPT_NUM_WORKERS_DESC - Static variable in class biolockj.Constants
-
- SCRIPT_PERMISSIONS - Static variable in class biolockj.Constants
-
- SCRIPT_PERMISSIONS_DESC - Static variable in class biolockj.Constants
-
- SCRIPT_PRINT_CONFIG - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
QIIME script to print environment configuration to qsub output file: "print_qiime_config.py"
- SCRIPT_STARTED - Static variable in class biolockj.Constants
-
File suffix appended to started script: "Started"
- SCRIPT_SUCCESS - Static variable in class biolockj.Constants
-
File suffix appended to successful scripts: "Success"
- SCRIPT_SUMMARIZE_BIOM - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
- SCRIPT_SUMMARIZE_TAXA - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
QIIME script used to produce taxonomy-level reports in the module output directory:
"summarize_taxa.py"
- SCRIPT_TIMEOUT - Static variable in class biolockj.Constants
-
- SCRIPT_TIMEOUT_DESC - Static variable in class biolockj.Constants
-
- SCRIPT_VALIDATE_MAPPING - Static variable in class biolockj.module.implicit.qiime.BuildQiimeMapping
-
QIIME script used to validate the QIIME mapping file format
- ScriptModule - Interface in biolockj.module
-
Classes that implement this interface are
- ScriptModuleImpl - Class in biolockj.module
-
Superclass for Java BioModules that will be called in separate instances of the application.
- ScriptModuleImpl() - Constructor for class biolockj.module.ScriptModuleImpl
-
- sendHostInfo(File) - Static method in class biolockj.util.SummaryUtil
-
Write the system host info.
- SeqFileValidator - Class in biolockj.module.seq
-
This BioModule validates fasta/fastq file formats are valid and enforces min/max read lengths.
- SeqFileValidator() - Constructor for class biolockj.module.seq.SeqFileValidator
-
- SeqModule - Interface in biolockj.module
-
Classes that implement this interface requires sequence files for input.
- SeqModuleImpl - Class in biolockj.module
-
Superclass for SeqModules that take sequence files as input for pre-processing prior to classification.
- SeqModuleImpl() - Constructor for class biolockj.module.SeqModuleImpl
-
- SequenceReadArchive - Class in biolockj.module.getData.sra
-
- SequenceReadArchive() - Constructor for class biolockj.module.getData.sra.SequenceReadArchive
-
- SequnceFormatException - Exception in biolockj.exception
-
SequnceFormatException is thrown if errors occur processing fasta/fastq sequence files.
- SequnceFormatException(File, String) - Constructor for exception biolockj.exception.SequnceFormatException
-
Create standard error to throw for fasta/fastq sequence file parsing errors.
- SequnceFormatException(String) - Constructor for exception biolockj.exception.SequnceFormatException
-
Create standard error to throw for fasta/fastq sequence file parsing errors.
- SeqUtil - Class in biolockj.util
-
This utility helps interact with FastA and FastQ sequence files.
- SET_SEED - Static variable in class biolockj.Constants
-
Config property "pipeline.setSeed"
- setAlias(String) - Method in interface biolockj.module.BioModule
-
- setAlias(String) - Method in class biolockj.module.BioModuleImpl
-
- setConfigProperty(String, Collection<?>, BioModule) - Static method in class biolockj.Config
-
Sets a property value in the props cache as a list
- setConfigProperty(String, Collection<?>) - Static method in class biolockj.Config
-
Sets a property value in the props cache as a list
- setConfigProperty(String, String, BioModule) - Static method in class biolockj.Config
-
Sets a property value in the props cache
- setConfigProperty(String, String) - Static method in class biolockj.Config
-
Sets a property value in the props cache
- setCount(long) - Method in interface biolockj.node.OtuNode
-
Set the number of reads for a sample ID that have this OTU assignment.
- setCount(long) - Method in class biolockj.node.OtuNodeImpl
-
- setDbCache(File) - Method in class biolockj.module.classifier.ClassifierModuleImpl
-
Set DB cache directory path on 1st access
- setFile(File) - Static method in class biolockj.util.MetaUtil
-
Set a new metadata file.
- setFilePathProperty(String, String, BioModule) - Static method in class biolockj.Config
-
- setFilePathProperty(String, String) - Static method in class biolockj.Config
-
- setFilePermissions(String, String) - Static method in class biolockj.Processor
-
- setLevel(String) - Method in class biolockj.node.JsonNode
-
Setter method for level
- setLine(String) - Method in interface biolockj.node.OtuNode
-
Set the classifier report line parsed to build this OTU node.
- setLine(String) - Method in class biolockj.node.OtuNodeImpl
-
Set line only if in DEBUG mode, so we can print OtuNode constructor inputs.
- setMasterConfig() - Method in class biolockj.pipelines.OtherPipelineImpl
-
Used to initial set the masterProps file object.
- setMultiplexedConfig() - Static method in class biolockj.util.DemuxUtil
-
- setNumHitsFieldName(String) - Static method in class biolockj.module.implicit.parser.ParserModuleImpl
-
When a module modifies the number of hits, the new counts must replace the old count fields.
- setNumReadFieldName(String) - Static method in class biolockj.module.implicit.RegisterNumReads
-
When a module modifies the number of reads, the new counts must replace the old count fields.
- setOrderedQiimeIDs(File) - Method in class biolockj.module.implicit.parser.r16s.QiimeParser
-
- setOtuCounts(Map<String, Long>) - Method in class biolockj.node.ParsedSample
-
Directly assign OtuCounts
- setParent(JsonNode) - Method in class biolockj.node.JsonNode
-
Setter method for parent
- setPipedir(File) - Method in class biolockj.launch.LaunchProcess
-
- setPipelineId() - Method in class biolockj.pipelines.OtherPipelineImpl
-
- setProjectName() - Method in class biolockj.pipelines.OtherPipelineImpl
-
- setSampleId(String) - Method in interface biolockj.node.OtuNode
-
Set the sample ID, parsed from file name or sequence header, to which this taxonomy assignment belongs.
- setSampleId(String) - Method in class biolockj.node.OtuNodeImpl
-
- setSampleId(String, String) - Static method in class biolockj.util.MetaUtil
-
- setSampleId(File, String) - Static method in class biolockj.util.MetaUtil
-
- setTaxa(String) - Method in class biolockj.node.JsonNode
-
Setter method for taxa
- setVerbose(boolean) - Static method in class biolockj.api.BioLockJ_API
-
- SH_EXT - Static variable in class biolockj.Constants
-
BioLockJ shell script file extension: ".sh"
- SH_EXT - Static variable in class biolockj.module.BioModuleImpl
-
BioLockJ shell script file extension constant: ".sh"
- SHANNON_COLUMN - Static variable in class biolockj.module.diversity.ShannonDiversity
-
- ShannonDiversity - Class in biolockj.module.diversity
-
- ShannonDiversity() - Constructor for class biolockj.module.diversity.ShannonDiversity
-
- showArgs(String, String[]) - Static method in class biolockj.launch.LaunchProcess
-
- showFileContents(File) - Static method in class biolockj.launch.ProgressUtil
-
- showFileContents(File, int, int) - Static method in class biolockj.launch.ProgressUtil
-
- showInfo(String[]) - Static method in class biolockj.util.BioLockJUtil
-
Print basic version or help info if requested.
Called by 1st line BioLockJ.java main() method
- showMap(TreeMap<String, String>) - Method in exception biolockj.exception.DockerVolumeException
-
- showUnusedProps() - Static method in class biolockj.Config
-
- showUserUpdates(String) - Static method in class biolockj.launch.ProgressUtil
-
Pass BioLockJ out/err stream lines.
- showValue(String) - Static method in exception biolockj.exception.ConfigException
-
- SILVA_CLASS_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
-
Silva class taxonomy level delimiter: "D_2__"
- SILVA_DOMAIN_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
-
Silva domain taxonomy level delimiter: "D_0__"
- SILVA_FAMILY_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
-
Silva family taxonomy level delimiter: "D_4__"
- SILVA_GENUS_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
-
Silva genus taxonomy level delimiter: "D_5__"
- SILVA_ORDER_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
-
Silva order taxonomy level delimiter: "D_3__"
- SILVA_PHYLUM_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
-
Silva phylum taxonomy level delimiter: "D_1__"
- SILVA_SPECIES_DELIM - Static variable in class biolockj.node.r16s.QiimeNode
-
Silva species taxonomy level delimiter: "D_6__"
- SimpleDockerMapper - Class in biolockj.util.paths
-
Introduced with BioLockJ v1.3.18.
- SimpleDockerMapper() - Constructor for class biolockj.util.paths.SimpleDockerMapper
-
- SIZE - Static variable in class biolockj.util.ValidationUtil
-
- SIZE_WITHIN_PERCENT - Static variable in class biolockj.util.ValidationUtil
-
Config property "validation.sizeWithinPercent" giving the percentage by which size is allow to
deviate and still be considered a valid match for the expectation.
- SPAWN_DOCKER_CONTAINER - Static variable in class biolockj.util.DockerUtil
-
Name of the bash script function used to generate a new Docker container: "spawnDockerContainer"
- SpecialPropertiesException - Exception in biolockj.exception
-
This type of exception is thrown if an error occurs while processing a special type of property such as "exe."
properties or defaultProps.
- SpecialPropertiesException(String) - Constructor for exception biolockj.exception.SpecialPropertiesException
-
- SpecialPropertiesException(String, String) - Constructor for exception biolockj.exception.SpecialPropertiesException
-
- SpecialPropertiesException(String, BioLockJException) - Constructor for exception biolockj.exception.SpecialPropertiesException
-
- SPECIES - Static variable in class biolockj.Constants
-
- SPECIES_DELIM - Static variable in class biolockj.node.OtuNodeImpl
-
Standard classifier output level delimiter for SPECIES
- SRA_ACC_LIST - Static variable in class biolockj.module.getData.sra.SequenceReadArchive
-
- SRA_ACC_LIST_DESC - Static variable in class biolockj.module.getData.sra.SequenceReadArchive
-
- SraDownload - Class in biolockj.module.getData.sra
-
- SraDownload() - Constructor for class biolockj.module.getData.sra.SraDownload
-
- SraMetaData - Class in biolockj.module.getData.sra
-
- SraMetaData() - Constructor for class biolockj.module.getData.sra.SraMetaData
-
- SraMetaDB - Class in biolockj.module.getData.sra
-
- SraMetaDB() - Constructor for class biolockj.module.getData.sra.SraMetaDB
-
- SRP - Static variable in class biolockj.module.getData.sra.SequenceReadArchive
-
- SRP_DESC - Static variable in class biolockj.module.getData.sra.SequenceReadArchive
-
- SrpSrrConverter - Class in biolockj.module.getData.sra
-
- SrpSrrConverter() - Constructor for class biolockj.module.getData.sra.SrpSrrConverter
-
- stageRootConfig() - Static method in class biolockj.util.NextflowUtil
-
Before any AWS or Nextflow functionality can be used, the Docker root user $HOME directory must be updated with
the EC2 user aws + Nextflow config.
- STANDARD_CONFIG_PATH - Static variable in class biolockj.Constants
-
Default
Config imported for all pipelines (if file exists)
- startNextflow(List<BioModule>) - Static method in class biolockj.util.NextflowUtil
-
Call this method to build the Nextflow main.nf for the current pipeline.
- startSpinner(String) - Static method in class biolockj.launch.ProgressUtil
-
- STATUS_MARK_KEY - Static variable in class biolockj.Constants
-
Key used in standard err messages indicating that this line should be shown to the user.
- STATUS_START_KEY - Static variable in class biolockj.Constants
-
Key used in standard err messages indicating that this line should be shown to the user.
- statusStrings - Static variable in class biolockj.util.ValidationUtil
-
- Step1 - Class in biolockj.module.hello_world
-
First set up a mostly-empty class.
- Step1() - Constructor for class biolockj.module.hello_world.Step1
-
- Step2 - Class in biolockj.module.hello_world
-
Start with the basic documentation.
- Step2() - Constructor for class biolockj.module.hello_world.Step2
-
- Step3 - Class in biolockj.module.hello_world
-
Even a very simple module probably uses at least one property.
- Step3() - Constructor for class biolockj.module.hello_world.Step3
-
- Step4 - Class in biolockj.module.hello_world
-
Specify the acceptable input data type for this module.
- Step4() - Constructor for class biolockj.module.hello_world.Step4
-
- Step5 - Class in biolockj.module.hello_world
-
- Step5() - Constructor for class biolockj.module.hello_world.Step5
-
- Stop - Class in biolockj.module
-
Stop a pipeline.
- Stop() - Constructor for class biolockj.module.Stop
-
- StopAfterPrecheck - Exception in biolockj.exception
-
When running in "precheck" mode, this is the mechanism that stops a pipeline from running.
- StopAfterPrecheck(String) - Constructor for exception biolockj.exception.StopAfterPrecheck
-
- StopAfterPrecheck() - Constructor for exception biolockj.exception.StopAfterPrecheck
-
- StopModuleException - Exception in biolockj.exception
-
- StopModuleException(Stop) - Constructor for exception biolockj.exception.StopModuleException
-
- stopNextflow() - Static method in class biolockj.util.NextflowUtil
-
Stop Nextflow process (required since parent Java process that ran BioLockJ pipeline will not halt until this
subprocess is finished.
- STRING_TYPE - Static variable in class biolockj.Properties
-
- subDirExists(BioModule, String) - Static method in class biolockj.util.ModuleUtil
-
Return TRUE if BioModule sub-directory exists
- submitJob(String[], String) - Static method in class biolockj.Processor
-
Instantiates a new
Processor.
String[] array used to control spacing between command/params.
As if executing on terminal args[0] args[1]...
- submitQuery(String, String) - Static method in class biolockj.Processor
-
Run script that expects a single result
- subProcAlive(Long) - Static method in class biolockj.Processor
-
Check if a specific process is alive
- Subprocess(String[], String) - Constructor for class biolockj.Processor.Subprocess
-
Execute the command args in a separate thread and log output with label.
- subProcsAlive() - Static method in class biolockj.Processor
-
Check if any Subprocess threads are still running.
- SUMMARIZE_TAXA_SUPPRESS_BIOM - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
-
- SUMMARY - Static variable in class biolockj.module.report.otu.CompileOtuCounts
-
Output file prefix: "summary"
- SummaryUtil - Class in biolockj.util
-
This module builds an execution summary for the pipeline which is printed to the log file and is be sent to the user
if the Email module is configured.
- SummaryUtil() - Constructor for class biolockj.util.SummaryUtil
-
- syncModuleLogs(ScriptModule) - Static method in class biolockj.util.LogUtil
-
Not used currently.
- SYSTEM_OUT_FLAG - Static variable in class biolockj.util.RuntimeParamUtil
-
Flag argument; if present, BioLockJ will print to System.out instead of Log for debugging early runtime errors.