comparison interproscan_render.R @ 1:035457a30aea draft

update

0:59d780043157

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

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


#------------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(specification_file = 'getopt_specification.csv', 
                                         tool_dir = Sys.getenv('TOOL_DIR')))
opt$X_t = Sys.getenv('TOOL_DIR')
#----------------------------------------------------

# for some unknow reason, directly using REPORT as the input value for output_file parameter
# in the render function can cause empty report file when the tool runs in batch mode.
# the solution is to render the rmarkdown to a explicitly specified file and then copy the
# file to ${REPORT}
render(paste0(TOOL_DIR, '/', RMD_NAME), 
       output_file = paste0(Sys.getenv('OUTPUT_DIR'), '/report.html'))
system(command = 'cp ${OUTPUT_DIR}/report.html ${OUTPUT_REPORT}')
#------------------------------------------

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

1:035457a30aea

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

library(getopt)
library(rmarkdown)
library(htmltools)
#------------------------------------------------


#------------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(specification_file = '/getopt_specification.csv', 
                                         tool_dir = Sys.getenv('TOOL_DIR')))
opt$X_t = Sys.getenv('TOOL_DIR')
#----------------------------------------------------

# for some unknow reason, directly using REPORT as the input value for output_file parameter
# in the render function can cause empty report file when the tool runs in batch mode.
# the solution is to render the rmarkdown to a explicitly specified file and then copy the
# file to ${REPORT}
render(paste0(TOOL_DIR, '/', RMD_NAME), 
       output_file = paste0(OUTPUT_DIR, '/report.html'))
system(command = 'cp ${X_d}/report.html ${X_o}')
#------------------------------------------

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