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## ---- define_modules ----
#' @param x number of sleep commands
sleep <- function(x, samplename){
cmd = list(sleep = sprintf("sleep %s && sleep %s;echo 'hello'",
abs(round(rnorm(x)*10, 0)),
abs(round(rnorm(x)*10, 0))))
flowmat = to_flowmat(cmd, samplename)
return(list(flowmat = flowmat))
}
#' @param x number of tmp commands
create_tmp <- function(x, samplename){
## Create 100 temporary files
tmp = sprintf("%s_tmp_%s", samplename, 1:x)
cmd = list(create_tmp = sprintf("head -c 100000 /dev/urandom > %s", tmp))
## --- convert the list into a data.frame
flowmat = to_flowmat(cmd, samplename)
return(list(flowmat = flowmat, outfiles = tmp))
}
#' @param x vector of files to merge
merge_size <- function(x, samplename){
## Merge them according to samples, 10 each
mergedfile = paste0(samplename, "_merged")
cmd_merge <- sprintf("cat %s > %s",
paste(x, collapse = " "), ## input files
mergedfile)
## get the size of merged files
cmd_size = sprintf("du -sh %s; echo 'MY shell:' $SHELL", mergedfile)
cmd = list(merge = cmd_merge, size = cmd_size)
## --- convert the list into a data.frame
flowmat = to_flowmat(cmd, samplename)
return(list(flowmat = flowmat, outfiles = mergedfile))
}
## ---- define_pipeline ----
#' @param x number of files to make
sleep_pipe <- function(x = 3, samplename = "samp1"){
## call the modules one by one...
out_sleep = sleep(x, samplename)
out_create_tmp = create_tmp(x, samplename)
out_merge_size = merge_size(out_create_tmp$outfiles, samplename)
## row bind all the commands
flowmat = rbind(out_sleep$flowmat,
out_create_tmp$flowmat,
out_merge_size$flowmat)
return(list(flowmat = flowmat, outfiles = out_merge_size$outfiles))
}
## ---- run_sleep_example ----
main <- function(){
#setwd("inst/examples"); ## cd to folder containing this script
require(flowr)
out = sleep_pipe(x = 3, "sample1")
flowmat = out$flowmat
def = to_flowdef(out$flowmat)
## change submission and dependency types
def$sub_type = c("scatter", "scatter", "serial", "serial")
def$dep_type = c("none", "serial", "gather", "serial")
## save a exmple plot
plot_flow(to_flow(flowmat, def), pdffile = "sleep_pipe.pdf", pdf = TRUE)
## save the data
write_sheet(def, "sleep_pipe.def")
## write a example output
write_sheet(flowmat, "sleep_pipe.tsv")
}