RdpClassifier#
Add to module run order:
#BioModule biolockj.module.classifier.r16s.RdpClassifier
Description#
Classify 16s samples with RDP.
Properties#
Properties are the name=value pairs in the configuration file.
RdpClassifier properties:#
| Property | Description |
|---|---|
| rdp.containerJar | string File path for RDP java executable JAR in docker. default: /app/classifier.jar |
| rdp.db | file path File path used to define an alternate RDP database default: null |
| rdp.hierCounts | boolean Generate TaxaTables using the RDP --hier_outfile option; uses the RdpHierParser instead of the standard RdpParser module. default: null |
| rdp.jar | file path File path for RDP java executable JAR default: null |
| rdp.javaParams | list the parameters to java when running rdp. default: null |
| rdp.minThresholdScore | numeric IFF rdp.hierCounts=Y, RdpClassifier will ignore OTU assignments below this threshold score (0-100) default: 80 |
| rdp.params | list parameters to use when running rdp. (must include "-f fixrank") default: -f fixrank |
General properties applicable to this module:#
| Property | Description |
|---|---|
| cluster.batchCommand | string Terminal command used to submit jobs on the cluster default: null |
| cluster.jobHeader | string Header written at top of worker scripts default: null |
| cluster.modules | list List of cluster modules to load at start of worker scripts default: null |
| cluster.prologue | string To run at the start of every script after loading cluster modules (if any) default: null |
| cluster.statusCommand | string Terminal command used to check the status of jobs on the cluster default: null |
| docker.saveContainerOnExit | boolean If Y, docker run command will NOT include the --rm flag default: null |
| docker.verifyImage | boolean In check dependencies, run a test to verify the docker image. default: null |
| pipeline.defaultSeqMerger | string Java class name for default module used combined paired read files default: biolockj.module.seq.PearMergeReads |
| script.defaultHeader | string Store default script header for MAIN script and locally run WORKER scripts. default: #!/bin/bash |
| script.numThreads | integer Used to reserve cluster resources and passed to any external application call that accepts a numThreads parameter. default: 8 |
| script.numWorkers | integer Set number of samples to process per script (if parallel processing) default: 1 |
| script.permissions | string Used as chmod permission parameter (ex: 774) default: 770 |
| script.timeout | integer Sets # of minutes before worker scripts times out. default: null |
Details#
version: 1.0.0 none
Adds modules#
pre-requisite modules
none found
post-requisite modules
biolockj.module.implicit.parser.r16s.RdpParser
Docker#
If running in docker, this module will run in a docker container from this image:
biolockjdevteam/rdp_classifier:v1.3.18
This can be modified using the following properties:
RdpClassifier.imageOwner
RdpClassifier.imageName
RdpClassifier.imageTag
Citation#
Module developed by Mike Sioda.