generate_markdown.R

setwd("~/LAB/TCGA/CancerMods/")
library(rmarkdown);
source("TCGAcurated.mRNAonly.R")
library(stringr)
library(bsselectR)
library(knitr)
library(magrittr)
library(DT)
library(plyr)

generateGenePage<-function(ens_id, gof_id, descr){
	rmarkdown::render("geneTab.Rmd", output_file=paste0(ens_id, ".html"), quiet=T, intermediates_dir=paste0("imd_",ens_id), params = list(gene = ens_id, gene_official= gof_id, gene_descr=descr))
	system(paste0("mkdir ", ens_id))
	system(paste0("mv ", ens_id, "*.png ", ens_id))
	system(paste0("mv ", ens_id, "*.html ", ens_id))
	system(paste0("rm -rf imd_",ens_id))
}

#generateGenePage("ENSG00000165819", "METTL3", "Some description of the gene")

enzymes<-read.csv("enzymes.txt", sep="\t", header=T, stringsAsFactors=F)


##############################################################
## Parallel implementation
##############################################################

## TODO: resolve sporadic pandoc error due to concurrent instances 

library(foreach)
library(doParallel)
cores=detectCores()

registerDoParallel(cores=14)
getDoParWorkers()

foreach(i=1:nrow(enzymes)) %dopar% {

	ensid_proc <- enzymes[i, "ENSEMBL_ID"]
	gene_proc <- enzymes[i, "Gene_name"]
	desc_proc <- enzymes[i, "Description"]
	if(!file.exists(paste0(ensid_proc, "/", ensid_proc, ".html"))){
		#message(ensid_proc)
		generateGenePage(ensid_proc, gene_proc, desc_proc)
	}
}

stopCluster(cl)

rmarkdown::render("index.Rmd", output_file="index.html")
system("rm -rf imd_*")

##############################################################
## Chunk processing
##############################################################
# (to run multiple single-thread instances of the script) 
#
# args = commandArgs(trailingOnly=TRUE)
# a=as.numeric(args[1])
# b=as.numeric(args[2])
#
# for(i in seq(a,b,1)){
#
#	ensid_proc <- enzymes[i, "ENSEMBL_ID"]
#	gene_proc <- enzymes[i, "Gene_name"]
#	desc_proc <- enzymes[i, "Description"]
#	
#	if(!file.exists(paste0(ensid_proc, "/", ensid_proc, ".html"))){
#		generateGenePage(ensid_proc, gene_proc, desc_proc)
#	}
# }
#
# rmarkdown::render("index.Rmd", output_file="index.html")
#
## EXTERNAL Commands for processing in chunks
##
## Rscript generate_markdown.R 1 35 2>&1 | tee A.log & 
## Rscript generate_markdown.R 36 71 2>&1 | tee B.log & 
## ...
## Rscript generate_markdown.R 288 310 2>&1 | tee I.log &
##
## ls ENSG00000* | grep .html | wc -l #check status of the make process