diff variant_simple_search_render.R @ 1:f8ac93c41720 draft

special characters

--- a/variant_simple_search_render.R	Tue Mar 20 11:29:28 2018 -0400
+++ b/variant_simple_search_render.R	Tue Mar 20 13:59:04 2018 -0400
@@ -10,6 +10,8 @@
 
 library(getopt)
 library(rmarkdown)
+library(jsonlite)
+library(DT)
 #------------------------------------------------
 
 
@@ -17,11 +19,11 @@
 # load helper function
 source(paste0(Sys.getenv('TOOL_DIR'), '/helper.R'))
 # import getopt specification matrix from a csv file
-spec_csv = paste0(Sys.getenv('TOOL_DIR'), '/getopt_specification.csv')
-opt = getopt(getopt_specification_matrix(spec_csv))
+opt = getopt(getopt_specification_matrix('/variant_simple_search.csv'))
 opt$X_t = Sys.getenv('TOOL_DIR')
 #----------------------------------------------------
 
+print(opt)
 
 #-----------using passed arguments in R 
 #           to define system environment variables---
@@ -34,7 +36,7 @@
 OUTPUT_DIR = opt$X_d
 TOOL_DIR =   opt$X_t
 OUTPUT_REPORT = opt$X_o
-RMD_NAME = ''
+RMD_NAME = 'variant_simple_search.Rmd'
 
 # create the output associated directory to store all outputs
 dir.create(OUTPUT_DIR, recursive = TRUE)