view fastq_dump_se_render.R @ 3:668be0a63172 draft default tip

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##============ Sink warnings and errors to a file ==============
## use the sink() function to wrap all code within it.
##==============================================================
zz = file('warnings_and_errors.txt')
sink(zz)
sink(zz, type = 'message')

#------------import libraries--------------------
options(stringsAsFactors = FALSE)

library(getopt)
library(rmarkdown)
library(stringr)
#------------------------------------------------


#------------get arguments into R--------------------
# load helper function
source(paste0(Sys.getenv('TOOL_DIR'), '/helper.R'))
# import getopt specification matrix from a csv file
opt = getopt(getopt_specification_matrix('getopt_specification.csv'))
opt$X_t = Sys.getenv('TOOL_DIR')
working_dir = getwd()
Sys.setenv(WORKING_DIR = working_dir)
#----------------------------------------------------


#-----------using passed arguments in R 
#           to define system environment variables---
do.call(Sys.setenv, opt[-1])
#----------------------------------------------------

#---------- often used variables ----------------
# OUTPUT_DIR: path to the output associated directory, which stores all outputs
# TOOL_DIR: path to the tool installation directory
OUTPUT_DIR = opt$X_d
TOOL_DIR =   opt$X_t
OUTPUT_REPORT = opt$X_o
RMD_NAME = 'fastq_dump_se.Rmd'


# create the output associated directory to store all outputs
dir.create(OUTPUT_DIR, recursive = TRUE)

#-----------------render Rmd--------------
render(paste0(TOOL_DIR, '/', RMD_NAME), output_file = OUTPUT_REPORT)
#------------------------------------------

#==============the end==============


##--------end of code rendering .Rmd templates----------------
sink()
##=========== End of sinking output=============================