Constant Field Values
Contents
fr.ens.*
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fr.ens.biologie.genomique.eoulsan.CommonHadoop Modifier and Type Constant Field Value public static final String
AWS_S3_ACCESS_KEY_ID_PARAM_KEY
"fs.s3n.awsAccessKeyId"
public static final String
AWS_S3_SECRET_ACCESS_KEY_PARAM_NAME
"fs.s3n.awsSecretAccessKey"
public static final int
CHECK_COMPLETION_TIME
5000
public static final String
HADOOP_PARAMETER_PREFIX
"hadoop.conf."
public static final String
HADOOP_REDUCER_TASK_COUNT_PARAMETER_NAME
"hadoop.reducer.task.count"
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fr.ens.biologie.genomique.eoulsan.Globals Modifier and Type Constant Field Value public static final String
APP_NAME
"Eoulsan"
public static final boolean
BYPASS_PLATFORM_CHECKING
false
public static final String
DEFAULT_FILE_ENCODING
"UTF-8"
public static final double
DESIGN_FILE_VERSION
1.1
public static final String
EOULSAN_TOOLS_WEBSITE_URL
"https://raw.githubusercontent.com/GenomicParisCentre/eoulsan-tools"
public static final int
FASTA_FILE_WIDTH
60
public static final int
INTERNET_CHECK_PORT
443
public static final String
INTERNET_CHECK_SERVER
"raw.githubusercontent.com"
public static final String
LICENSE_TXT
"This program is developed under the GNU Lesser General Public License version 2.1 or later and CeCILL-C."
public static final String
LOG_EXTENSION
".log"
public static final int
MINIMAL_JAVA_VERSION_REQUIRED
8
public static final boolean
OBFUSCATE_DESIGN_DEFAULT
true
public static final boolean
OBFUSCATE_DESIGN_REMOVE_REPLICATE_INFO_DEFAULT
true
public static final String
OTHER_LOG_FILENAME
"additional.log"
public static final String
OUTPUT_TREE_TYPE_DEFAULT
"step"
public static final boolean
SAVE_WORKFLOW_IMAGE_DEFAULT
true
public static final boolean
STANDARD_EXTERNAL_MODULES_ENABLED_DEFAULT
true
public static final boolean
STD_OUTPUT_DEFAULT
false
public static final String
STEP_LOG_EXTENSION
".step.log"
public static final String
STEP_OUTPUT_DIRECTORY_SUFFIX
"_output"
public static final String
STEP_RESULT_EXTENSION
".step.result"
public static final String
STEP_RESULT_OLD_FORMAT_EXTENSION
".log"
public static final String
TASK_CONTEXT_EXTENSION
".task.context"
public static final String
TASK_DATA_EXTENSION
".task.data"
public static final String
TASK_DONE_EXTENSION
".task.done"
public static final String
TASK_JOB_ID
".task.job.id"
public static final String
TASK_LOG_EXTENSION
".task.log"
public static final String
TASK_RESULT_EXTENSION
".task.result"
public static final String
TASK_STDERR_EXTENSION
".task.err"
public static final String
TASK_STDOUT_EXTENSION
".task.out"
public static final String
UI_NAME_DEFAULT
"lanterna"
public static final boolean
USE_OLD_EOULSAN_RESULT_FORMAT_DEFAULT
false
public static final int
ZOOKEEPER_DEFAULT_PORT_DEFAULT
2181
public static final int
ZOOKEEPER_SESSION_TIMEOUT_DEFAULT
10000
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fr.ens.biologie.genomique.eoulsan.Main Modifier and Type Constant Field Value public static final String
EOULSAN_CLASSPATH_JVM_ARG
"eoulsan.classpath"
public static final String
EOULSAN_MEMORY
"eoulsan.memory"
public static final String
EOULSAN_PATH
"eoulsan.path"
public static final String
EOULSAN_SCRIPT
"eoulsan.launch.script.path"
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fr.ens.biologie.genomique.eoulsan.Settings Modifier and Type Constant Field Value public static final String
DATA_FORMAT_PATH_KEY
"main.format.path"
public static final String
GALAXY_TOOL_PATH_KEY
"main.galaxy.tool.path"
public static final String
STANDARD_EXTERNAL_MODULES_ENABLED_KEY
"main.standard.external.modules.enabled"
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fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction Modifier and Type Constant Field Value public static final String
ACTION_NAME
"clusterexec"
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fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction Modifier and Type Constant Field Value public static final String
ACTION_NAME
"clustertask"
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fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction Modifier and Type Constant Field Value public static final String
ACTION_NAME
"createdesign"
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fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction Modifier and Type Constant Field Value public static final String
ACTION_NAME
"createhadoopjar"
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fr.ens.biologie.genomique.eoulsan.actions.ExecAction Modifier and Type Constant Field Value public static final String
ACTION_NAME
"exec"
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fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction Modifier and Type Constant Field Value public static final String
ACTION_NAME
"execjarhadoop"
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fr.ens.biologie.genomique.eoulsan.actions.FormatsAction Modifier and Type Constant Field Value public static final String
ACTION_NAME
"formats"
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fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction Modifier and Type Constant Field Value public static final String
ACTION_NAME
"hadoopexec"
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fr.ens.biologie.genomique.eoulsan.actions.InfoAction Modifier and Type Constant Field Value public static final String
ACTION_NAME
"info"
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fr.ens.biologie.genomique.eoulsan.actions.ModulesAction Modifier and Type Constant Field Value public static final String
ACTION_NAME
"modules"
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fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.Counters Modifier and Type Constant Field Value public static final String
ENTRIES_READ
"Entries Read"
public static final String
ENTRIES_WRITTEN
"Entries Written"
public static final String
INPUT_ENTRIES
"Input Entries"
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fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader Modifier and Type Constant Field Value public static final String
MAX_LINE_LENGTH
"mapreduce.input.linerecordreader.line.maxlength"
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fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker Modifier and Type Constant Field Value public static final String
GENOME_DESCRIPTION
"genome_description"
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fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker Modifier and Type Constant Field Value public static final int
MAX_READS_TO_CHECK
1000
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fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder Modifier and Type Constant Field Value public static final String
DEFAULT_SINGLE_INPUT_PORT_NAME
"input"
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fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder Modifier and Type Constant Field Value public static final String
DEFAULT_SINGLE_OUTPUT_PORT_NAME
"output"
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fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.HTCondorTaskScheduler Modifier and Type Constant Field Value public static final String
SCHEDULER_NAME
"htcondor"
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fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.PBSProTaskScheduler Modifier and Type Constant Field Value public static final String
SCHEDULER_NAME
"pbspro"
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fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.SLURMTaskScheduler Modifier and Type Constant Field Value public static final String
SCHEDULER_NAME
"slurm"
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fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TGCCTaskScheduler Modifier and Type Constant Field Value public static final String
SCHEDULER_NAME
"tgcc"
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fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TORQUETaskScheduler Modifier and Type Constant Field Value public static final String
SCHEDULER_NAME
"torque"
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fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow Modifier and Type Constant Field Value protected static final String
WORKFLOW_COPY_FILENAME
"workflow.xml"
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fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser Modifier and Type Constant Field Value public static final String
DESIGN_FILE_PATH_CONSTANT_NAME
"design.file.path"
public static final String
JOB_ID_CONSTANT_NAME
"job.id"
public static final String
JOB_PATH_CONSTANT_NAME
"job.path"
public static final String
JOB_UUID_CONSTANT_NAME
"job.uuid"
public static final String
OUTPUT_PATH_CONSTANT_NAME
"output.path"
public static final String
WORKFLOW_FILE_PATH_CONSTANT_NAME
"workflow.file.path"
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fr.ens.biologie.genomique.eoulsan.data.DataFile Modifier and Type Constant Field Value public static final String
separator
"/"
public static final char
separatorChar
47
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fr.ens.biologie.genomique.eoulsan.data.DataMetadata Modifier and Type Constant Field Value public static final String
FASTQ_FORMAT_KEY
"FastqFormat"
public static final String
PAIRED_END_KEY
"pairedend"
public static final String
SAMPLE_ID_KEY
"SampleId"
public static final String
SAMPLE_NAME_KEY
"SampleName"
public static final String
SAMPLE_NUMBER_KEY
"SampleNumber"
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fr.ens.biologie.genomique.eoulsan.data.protocols.AnnotationDataProtocol Modifier and Type Constant Field Value public static final String
PROTOCOL_NAME
"annotation"
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fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol Modifier and Type Constant Field Value public static final String
PROTOCOL_NAME
"file"
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fr.ens.biologie.genomique.eoulsan.data.protocols.FTPPathDataProtocol Modifier and Type Constant Field Value public static final String
PROTOCOL_NAME
"ftp"
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fr.ens.biologie.genomique.eoulsan.data.protocols.FTPURLDataProtocol Modifier and Type Constant Field Value public static final String
PROTOCOL_NAME
"ftp"
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fr.ens.biologie.genomique.eoulsan.data.protocols.GenomeDataProtocol Modifier and Type Constant Field Value public static final String
PROTOCOL_NAME
"genome"
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fr.ens.biologie.genomique.eoulsan.data.protocols.GFFDataProtocol Modifier and Type Constant Field Value public static final String
PROTOCOL_NAME
"gff"
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fr.ens.biologie.genomique.eoulsan.data.protocols.GTFDataProtocol Modifier and Type Constant Field Value public static final String
PROTOCOL_NAME
"gtf"
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fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol Modifier and Type Constant Field Value public static final String
PROTOCOL_NAME
"hdfs"
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fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPPathDataProtocol Modifier and Type Constant Field Value public static final String
PROTOCOL_NAME
"http"
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fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSPathDataProtocol Modifier and Type Constant Field Value public static final String
PROTOCOL_NAME
"https"
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fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSURLDataProtocol Modifier and Type Constant Field Value public static final String
PROTOCOL_NAME
"https"
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fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPURLDataProtocol Modifier and Type Constant Field Value public static final String
PROTOCOL_NAME
"http"
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fr.ens.biologie.genomique.eoulsan.design.DesignMetadata Modifier and Type Constant Field Value public static final String
ADDITIONAL_ANNOTATION_FILE_KEY
"AdditionalAnnotationFile"
public static final String
GENOME_FILE_KEY
"GenomeFile"
public static final String
GFF_FILE_KEY
"GffFile"
public static final String
GTF_FILE_KEY
"GtfFile"
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fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata Modifier and Type Constant Field Value public static final String
BUILD_CONTRAST_KEY
"buildContrast"
public static final String
COMPARISONS_KEY
"comparisons"
public static final String
CONTRAST_FILE_KEY
"contrastFile"
public static final String
CONTRAST_KEY
"contrast"
public static final String
DESIGN_FILE_KEY
"designFile"
public static final String
MODEL_KEY
"model"
public static final String
REFERENCE_KEY
"reference"
public static final String
SKIP_KEY
"skip"
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fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata Modifier and Type Constant Field Value public static final String
CONDITION_KEY
"Condition"
public static final String
REFERENCE_KEY
"Reference"
public static final String
REP_TECH_GROUP_KEY
"RepTechGroup"
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fr.ens.biologie.genomique.eoulsan.design.Sample Modifier and Type Constant Field Value public static final String
SAMPLE_ID_FIELD
"SampleId"
public static final String
SAMPLE_NAME_FIELD
"SampleName"
public static final String
SAMPLE_NUMBER_FIELD
"SampleNumber"
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fr.ens.biologie.genomique.eoulsan.design.SampleMetadata Modifier and Type Constant Field Value public static final String
COMMENT_KEY
"Comment"
public static final String
CONDITION_KEY
"Condition"
public static final String
DATE_KEY
"Date"
public static final String
DESCRIPTION_KEY
"Description"
public static final String
FASTQ_FORMAT_KEY
"FastqFormat"
public static final String
OPERATOR_KEY
"Operator"
public static final String
READS_KEY
"Reads"
public static final String
REFERENCE_KEY
"Reference"
public static final String
REP_TECH_GROUP_KEY
"RepTechGroup"
public static final String
SERIAL_NUMBER_KEY
"SerialNumber"
public static final String
UUID_KEY
"UUID"
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fr.ens.biologie.genomique.eoulsan.galaxytools.CheetahInterpreter Modifier and Type Constant Field Value public static final String
CALL_METHOD
"galaxy_dict.get"
public static final String
PYTHON_VARIABLES_DICT_NAME
"galaxy_dict"
public static final String
VAR_CMD_NAME
"cmd"
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fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement Modifier and Type Constant Field Value public static final String
TYPE
"boolean"
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fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement Modifier and Type Constant Field Value public static final String
TYPE
"boolean"
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fr.ens.biologie.genomique.eoulsan.galaxytools.elements.DataToolElement Modifier and Type Constant Field Value public static final String
TAG_NAME
"data"
public static final String
TYPE
"data"
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fr.ens.biologie.genomique.eoulsan.galaxytools.elements.FloatParameterToolElement Modifier and Type Constant Field Value public static final String
TYPE
"float"
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fr.ens.biologie.genomique.eoulsan.galaxytools.elements.IntegerParameterToolElement Modifier and Type Constant Field Value public static final String
TYPE
"integer"
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fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement Modifier and Type Constant Field Value public static final String
TYPE
"select"
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fr.ens.biologie.genomique.eoulsan.galaxytools.elements.TextParameterToolElement Modifier and Type Constant Field Value public static final String
TYPE
"text"
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fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElement Modifier and Type Constant Field Value public static final String
SEP
"."
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fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DefaultExecutorInterpreter Modifier and Type Constant Field Value public static final String
INTERPRETER_NAME
"default"
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fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter Modifier and Type Constant Field Value public static final String
INTERPRETER_NAME
"docker"
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fr.ens.biologie.genomique.eoulsan.io.FileCharsets Modifier and Type Constant Field Value public static final String
ASCII_ENCODING
"US-ASCII"
public static final String
LATIN1_FILE_ENCODING
"ISO-8859-1"
public static final String
UTF8_FILE_ENCODING
"UTF-8"
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fr.ens.biologie.genomique.eoulsan.modules.CheckerModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"checker"
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fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule Modifier and Type Constant Field Value public static final String
FORMAT_PARAMETER
"format"
public static final String
MODULE_NAME
"_copyinputformat"
public static final String
OUTPUT_COMPRESSION_PARAMETER
"output.compression"
public static final String
OUTPUT_COMPRESSIONS_ALLOWED_PARAMETER
"output.compressions.allowed"
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fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule Modifier and Type Constant Field Value public static final String
FORMATS_PARAMETER
"formats"
public static final String
MODULE_NAME
"_copyoutputformat"
public static final String
PORTS_PARAMETER
"ports"
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fr.ens.biologie.genomique.eoulsan.modules.DesignModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"design"
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fr.ens.biologie.genomique.eoulsan.modules.FailModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"fail"
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fr.ens.biologie.genomique.eoulsan.modules.FakeModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"fake"
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fr.ens.biologie.genomique.eoulsan.modules.FirstModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"first"
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fr.ens.biologie.genomique.eoulsan.modules.ImportModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"import"
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fr.ens.biologie.genomique.eoulsan.modules.MergerModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"merger"
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fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"requirementinstaller"
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fr.ens.biologie.genomique.eoulsan.modules.SplitterModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"splitter"
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fr.ens.biologie.genomique.eoulsan.modules.TechnicalReplicateMergerModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"technicalreplicatemerger"
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fr.ens.biologie.genomique.eoulsan.modules.TerminalModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"terminal"
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fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule Modifier and Type Constant Field Value protected static final String
COUNTER_GROUP
"rmdup"
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fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module Modifier and Type Constant Field Value protected static final String
COUNTER_GROUP
"peak_calling"
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fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule Modifier and Type Constant Field Value protected static final String
COUNTER_GROUP
"sam_stats"
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fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module Modifier and Type Constant Field Value public static final String
MODULE_NAME
"deseq2"
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fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"diffanaresultsannotation"
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fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization Modifier and Type Constant Field Value protected static final String
NORMALIZATION_FUNCTIONS
"/DESeq1/normalization_anaDiff_RNAseq_Functions.R"
protected static final String
TARGET_CREATION
"/DESeq1/targetCreation.Rnw"
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fr.ens.biologie.genomique.eoulsan.modules.diffana.RModuleCommonConfiguration Modifier and Type Constant Field Value public static final String
DOCKER_IMAGE_PARAMETER
"docker.image"
public static final String
EXECUTION_MODE_PARAMETER
"r.execution.mode"
public static final String
RSERVE_SERVER_PARAMETER
"rserve.servername"
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fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule Modifier and Type Constant Field Value protected static final String
COUNTER_GROUP
"expression"
public static final String
COUNTER_PARAMETER_NAME
"counter"
public static final String
FEATURES_FILE_FORMAT_PARAMETER_NAME
"features.file.format"
public static final String
MODULE_NAME
"expression"
public static final String
OUTPUT_FILE_FORMAT_PARAMETER_NAME
"output.file.format"
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fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule Modifier and Type Constant Field Value public static final String
COUNTER_GROUP
"expressionresultsannotation"
public static final String
MODULE_NAME
"expressionresultsannotation"
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fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule Modifier and Type Constant Field Value public static final String
FASTQC_CASAVA_PARAMETER_NAME
"fastqc.casava"
public static final String
FASTQC_EXPGROUP_PARAMETER_NAME
"fastqc.expgroup"
public static final String
FASTQC_KMER_SIZE_PARAMETER_NAME
"fastqc.kmer.size"
public static final String
FASTQC_NOFILTER_PARAMETER_NAME
"fastqc.nofilter"
public static final String
FASTQC_NOGROUP_PARAMETER_NAME
"fastqc.nogroup"
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fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"dummygenerator"
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fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"genericstoragegenerator"
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fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"genomedescgenerator"
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fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"genericindexgenerator"
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fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"gfffastagenerator"
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fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"minimap2indexgenerator"
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fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"starindexgenerator"
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fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule Modifier and Type Constant Field Value protected static final String
COUNTER_GROUP
"bam2sam"
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fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule Modifier and Type Constant Field Value protected static final String
GENOME_DESCRIPTION_PORT_NAME
"genomedescription"
protected static final int
HADOOP_TIMEOUT
3600000
protected static final String
MAPPER_INDEX_PORT_NAME
"mapperindex"
public static final String
MODULE_NAME
"filterandmap"
protected static final String
READS_PORT_NAME
"reads"
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fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule Modifier and Type Constant Field Value protected static final String
COUNTER_GROUP
"reads_filtering"
protected static final String
MODULE_NAME
"filterreads"
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fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule Modifier and Type Constant Field Value protected static final String
COUNTER_GROUP
"reads_mapping"
protected static final String
GENOME_DESCRIPTION_PORT_NAME
"genomedescription"
public static final String
HADOOP_THREADS_PARAMETER_NAME
"hadoop.threads"
public static final int
HADOOP_TIMEOUT
3600000
public static final String
LOCAL_THREADS_PARAMETER_NAME
"local.threads"
public static final String
MAPPER_ARGUMENTS_PARAMETER_NAME
"mapper.arguments"
public static final String
MAPPER_DOCKER_IMAGE_PARAMETER_NAME
"mapper.docker.image"
public static final String
MAPPER_FLAVOR_PARAMETER_NAME
"mapper.flavor"
protected static final String
MAPPER_INDEX_PORT_NAME
"mapperindex"
public static final String
MAPPER_NAME_PARAMETER_NAME
"mapper"
public static final String
MAPPER_VERSION_PARAMETER_NAME
"mapper.version"
public static final String
MAX_LOCAL_THREADS_PARAMETER_NAME
"max.local.threads"
public static final String
MODULE_NAME
"mapreads"
protected static final String
READS_PORT_NAME
"reads"
public static final String
USE_BUNDLED_BINARIES_PARAMETER_NAME
"mapper.use.bundled.binares"
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fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule Modifier and Type Constant Field Value protected static final String
COUNTER_GROUP
"sam2bam"
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fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule Modifier and Type Constant Field Value protected static final String
COUNTER_GROUP
"sam2fastq"
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fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule Modifier and Type Constant Field Value protected static final String
COUNTER_GROUP
"sam_filtering"
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fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule Modifier and Type Constant Field Value protected static final String
COUNTER_GROUP
"splice2bed"
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fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils Modifier and Type Constant Field Value public static final String
HEADERMERGER_INPUTS_PROPERTY
"hadoopbam.headermerger.inputs"
public static final String
WORK_FILENAME_PROPERTY
"hadoopbam.work.filename"
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fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule Modifier and Type Constant Field Value public static final String
MODULE_NAME
"_copy_design_params_to_output"
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fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp.DuplicationException Modifier and Type Constant Field Value public static final int
ERROR_CODE
-2
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fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload Modifier and Type Constant Field Value protected static final String
STEP_NAME
"defineformatstodownload"
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fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule Modifier and Type Constant Field Value public static final String
DATAFORMATS_TO_DOWNLOAD_SETTING
"dataformat.to.download"
public static final String
MODULE_NAME
"_download"
public static final String
NO_HDFS_DOWNLOAD
"no.hdfs.download"
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fr.ens.biologie.genomique.eoulsan.modules.multiqc.ExpressionInputPreprocessor Modifier and Type Constant Field Value public static final String
REPORT_NAME
"expression"
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fr.ens.biologie.genomique.eoulsan.modules.multiqc.FastQCInputPreprocessor Modifier and Type Constant Field Value public static final String
REPORT_NAME
"fastqc"
-
fr.ens.biologie.genomique.eoulsan.modules.multiqc.FeatureCountsInputPreprocessor Modifier and Type Constant Field Value public static final String
REPORT_NAME
"featurecounts"
-
fr.ens.biologie.genomique.eoulsan.modules.multiqc.MapperInputPreprocessor Modifier and Type Constant Field Value public static final String
REPORT_NAME
"mapreads"
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fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement Modifier and Type Constant Field Value protected static final String
INSTALLABLE_PARAMETER
"installable"
public static final String
NAME_PARAMETER
"name"
protected static final String
OPTIONAL_PARAMETER
"optional"
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fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement Modifier and Type Constant Field Value public static final String
REQUIREMENT_NAME
"docker"
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fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement Modifier and Type Constant Field Value public static final String
REQUIREMENT_NAME
"path"
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fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement Modifier and Type Constant Field Value public static final String
REQUIREMENT_NAME
"rserve"
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fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock Modifier and Type Constant Field Value public static final int
ANY_VERSION
-1
-
fr.ens.biologie.genomique.eoulsan.util.r.DockerRExecutor Modifier and Type Constant Field Value public static final String
REXECUTOR_NAME
"docker"
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fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor Modifier and Type Constant Field Value protected static final String
DEFAULT_R_LANG
"C"
protected static final String
LANG_ENVIRONMENT_VARIABLE
"LANG"
public static final String
REXECUTOR_NAME
"process"
public static final String
RSCRIPT_EXECUTABLE
"Rscript"
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fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor Modifier and Type Constant Field Value public static final String
REXECUTOR_NAME
"rserve"