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.