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