Rmarkdown#

Add to module run order:
#BioModule biolockj.module.diy.Rmarkdown

Description#

Render a custom R markdown.

Properties#

Properties are the name=value pairs in the configuration file.

Rmarkdown properties:#

Property Description
rmarkdown.resources list of file paths
path to one or more files to be copied to the module resource folder.
default: null
rmarkdown.rmarkdown file path
path to an R markdown file (.Rmd) to be rendered.
default: null

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
exe.Rscript executable
Path for the "Rscript" executable; if not supplied, any script that needs the Rscript command will assume it is on the PATH.
default: null
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: 0.0.0 none

Adds modules#

pre-requisite modules
none found
post-requisite modules
none found

Docker#

If running in docker, this module will run in a docker container from this image:

rocker/r-rmd:latest

This can be modified using the following properties:
Rmarkdown.imageOwner
Rmarkdown.imageName
Rmarkdown.imageTag

Citation#

Module created by Ivory Blakley
BioLockJ v1.4.2